REBASE--a database for DNA restriction and modification: enzymes, genes and genomesRichard J Roberts
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 38:D234-6. 2010
..The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email...
- One step at a time: endoplasmic reticulum-associated degradation
Shruthi S Vembar
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
Nat Rev Mol Cell Biol 9:944-57. 2008
..Here, we summarize our current understanding of each step during ERAD, with emphasis on the factors that catalyse distinct activities...
Highly efficient endogenous human gene correction using designed zinc-finger nucleasesFyodor D Urnov
Sangamo BioSciences, Inc, Pt. Richmond Tech Center 501, Canal Blvd, Suite A100 Richmond, California 94804, USA
Nature 435:646-51. 2005
..We observe comparably high frequencies in human T cells, raising the possibility of strategies based on zinc-finger nucleases for the treatment of disease...
- SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity
Estela Jacinto
Department of Physiology and Biophysics, UMDNJ Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
Cell 127:125-37. 2006
..Our findings reveal that the SIN1-rictor-mTOR function in Akt-Ser473 phosphorylation is required for TORC2 function in cell survival but is dispensable for TORC1 function...
N-terminal acetylation of cellular proteins creates specific degradation signalsCheol Sang Hwang
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
Science 327:973-7. 2010
..Several examined proteins of diverse functions contained these N-terminal degrons, termed AcN-degrons, which are a prevalent class of degradation signals in cellular proteins...
- Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs
Justin Ashworth
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Nucleic Acids Res 38:5601-8. 2010
....
- A "silent" polymorphism in the MDR1 gene changes substrate specificity
Chava Kimchi-Sarfaty
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
Science 315:525-8. 2007
....
- Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs
Janine Mok
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Sci Signal 3:ra12. 2010
..Together, these results elucidate how kinase catalytic domains recognize their phosphorylation targets and suggest general avenues for the identification of previously unknown kinase substrates across eukaryotes...
- Protein kinase CK2: structure, regulation and role in cellular decisions of life and death
David W Litchfield
Department of Biochemistry, Siebens Drake Research Institute, University of Western Ontario, London, Ontario, Canada N6A 5C1
Biochem J 369:1-15. 2003
..Furthermore, this anti-apoptotic function of CK2 may contribute to its ability to participate in transformation and tumorigenesis...
- Substrate-specific activation of sirtuins by resveratrol
Matt Kaeberlein
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
J Biol Chem 280:17038-45. 2005
..In light of these findings, the mechanism accounting for putative longevity effects of resveratrol should be reexamined...
- Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase Balpha
D R Alessi
Medical Research Council Protein Phosphorylation Unit, Department of Biochemistry, University of Dundee, Dundee, DD1 4HN, Scotland
Curr Biol 7:261-9. 1997
..The phosphorylation of both residues is required for maximal activation of PKB. The kinases that phosphorylate PKB are, however, unknown...
- A novel heterodimeric cysteine protease is required for interleukin-1 beta processing in monocytes
N A Thornberry
Department of Biochemistry, Merck Research Laboratories, Rahway, New Jersey 07065
Nature 356:768-74. 1992
..Selective inhibition of the enzyme in human blood monocytes blocks production of mature IL-1 beta, indicating that it is a potential therapeutic target...
- Identification of Holliday junction resolvases from humans and yeast
Stephen C Y Ip
Genetic Recombination Laboratory, Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
Nature 456:357-61. 2008
..Recombinant GEN1 and Yen1 resolve Holliday junctions by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated...
- HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues
Tobias Krojer
Research Institute of Molecular Pathology, Vienna, Austria
Nat Struct Mol Biol 17:844-52. 2010
..Implications for protein quality control and regulation of oligomeric enzymes are discussed...
- Maintaining a sense of direction during long-range communication on DNA
Mark D Szczelkun
DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
Biochem Soc Trans 38:404-9. 2010
..The generality of this mechanism to other ATP-dependent communication processes such as mismatch repair is also discussed...
- Acetylation: a regulatory modification to rival phosphorylation?
T Kouzarides
Wellcome CRC Institute, Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QR, UK
EMBO J 19:1176-9. 2000
..is acetylation a modification analogous to phosphorylation? This review sets out what we know about the broader substrate specificity and regulation of acetyl- ases and goes on to compare acetylation with the process of phosphorylation.
- An unbiased genome-wide analysis of zinc-finger nuclease specificity
Richard Gabriel
Department of Translational Oncology, National Center for Tumor Diseases NCT and German Cancer Research Center DKFZ, Heidelberg, Germany
Nat Biotechnol 29:816-23. 2011
..Comprehensive mapping of ZFN activity in vivo will facilitate the broad application of these reagents in translational research...
- Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity
Eva Maria Händel
Charite Medical School, Institute of Virology CBF, Berlin, Germany
Mol Ther 17:104-11. 2009
..In summary, both sequence and length of the inter-domain linker determine ZFN activity and target-site specificity, and are therefore important parameters to account for when designing ZFNs for genome editing...
- Autotaxin has lysophospholipase D activity leading to tumor cell growth and motility by lysophosphatidic acid production
Makiko Umezu-Goto
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
J Cell Biol 158:227-33. 2002
..It also provides potential novel targets for therapy of pathophysiological states including cancer...
- Design of protein-interaction specificity gives selective bZIP-binding peptides
Gevorg Grigoryan
MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Nature 458:859-64. 2009
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- Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations
R B Pearson
Methods Enzymol 200:62-81. 1991
- A Legionella pneumophila-translocated substrate that is required for growth within macrophages and protection from host cell death
Rita K Laguna
Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA
Proc Natl Acad Sci U S A 103:18745-50. 2006
..Defective intracellular growth of the sdhA(-) mutant could be partially suppressed by the action of caspase inhibitors, but caspase-independent cell death pathways eventually aborted replication of the mutant...
- Regulation of p53 activity through lysine methylation
Sergei Chuikov
Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
Nature 432:353-60. 2004
..The crystal structure of a ternary complex of Set9 with a p53 peptide and the cofactor product S-adenosyl-l-homocysteine (AdoHcy) provides the molecular basis for recognition of p53 by this lysine methyltransferase...
- Synthesis of novel lipids in Saccharomyces cerevisiae by heterologous expression of an unspecific bacterial acyltransferase
Rainer Kalscheuer
, , , Germany
Appl Environ Microbiol 70:7119-25. 2004
..calcoaceticus ADP1, indicating the broad biocatalytic potential of this enzyme for biotechnological production of a large variety of lipids in vivo in prokaryotic as well as eukaryotic expression hosts...
- Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands
Kelly L Sanders
Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
Nucleic Acids Res 37:2105-15. 2009
..The latter extends the range of enzymes for nicking specified strands at specific sequences, and may facilitate further applications of FokI in gene targeting...
- Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
Yujiang Shi
Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
Cell 119:941-53. 2004
..The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases...
- Enzymatic action of prostate-specific antigen (PSA or hK3): substrate specificity and regulation by Zn(2+), a tight-binding inhibitor
J Malm
Section for Clinical Chemistry, Department of Laboratory Medicine, Lund University, University Hospital Malmo, Malmo, Sweden
Prostate 45:132-9. 2000
..We characterized the substrate specificity and zinc-mediated inhibition of PSA.
- Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery
Stephane Angers
Howard Hughes Medical Institute, University of Washington, School of Medicine, Box 357280, Seattle, Washington 98195, USA
Nature 443:590-3. 2006
..Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes...
- Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
Pilar Redondo
Macromolecular Crystallography Group, Spanish National Cancer Research Centre CNIO, c Melchor Fdez Almagro 3, 28029 Madrid, Spain
Nature 456:107-11. 2008
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- Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector
Li Xu
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
PLoS Pathog 6:e1000822. 2010
..Our results indicate that direct targeting of v-ATPase by secreted proteins constitutes a virulence strategy for L. pneumophila, a vacuolar pathogen of macrophages and amoebae...
- Mammalian wax biosynthesis. II. Expression cloning of wax synthase cDNAs encoding a member of the acyltransferase enzyme family
Jeffrey B Cheng
Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
J Biol Chem 279:37798-807. 2004
..The data suggest that wax monoester synthesis in mammals involves a two step biosynthetic pathway catalyzed by fatty acyl-CoA reductase and wax synthase enzymes...
- Substrate specificities of caspase family proteases
R V Talanian
BASF Bioresearch Corp, Worcester, Massachusetts 01605, USA
J Biol Chem 272:9677-82. 1997
..The results also suggest the design of optimal peptidic substrates and inhibitors...
- Protease degradomics: mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors
Christopher M Overall
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
Biol Chem 385:493-504. 2004
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- Analysis of the DNA substrate specificity of the human BACH1 helicase associated with breast cancer
Rigu Gupta
Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
J Biol Chem 280:25450-60. 2005
We have investigated the DNA substrate specificity of BACH1 (BRCA1-associated C-terminal helicase). The importance of various DNA structural elements for efficient unwinding by purified recombinant BACH1 helicase was examined...
- Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease
Audrey McConnell Smith
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, North Seattle, WA 98109, USA
Proc Natl Acad Sci U S A 106:5099-104. 2009
..The cleavage mechanism, DNA-binding affinity, and substrate specificity profile of the nickase are similar to the wild-type enzyme...
- A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
Paul C Blainey
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 103:5752-7. 2006
..5 kcal/mol (1 kcal = 4.2 kJ). This nearly barrierless Brownian sliding indicates that DNA glycosylases locate lesion bases by a massively redundant search in which the enzyme selectively binds 8-oxoguanine under kinetic control...
- Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen
Shawn E Lupold
Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 2101, USA
Cancer Res 62:4029-33. 2002
..These aptamers may be used clinically as NAALADase inhibitors or be modified to carry imaging agents and therapeutic agents directed to prostate cancer cells...
- Exploitation of binding energy for catalysis and design
Summer B Thyme
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 461:1300-4. 2009
..Our results illustrate how classical enzymology and modern protein design can each inform the other...
- Updated biological roles for matrix metalloproteinases and new "intracellular" substrates revealed by degradomics
Georgina S Butler
Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
Biochemistry 48:10830-45. 2009
..Here we review progress made in the field of degradomics and present a current view of the MMP degradome...
- Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases
Stephanie A Nick McElhinny
Laboratory of Molecular Genetics and Laboratory of Structural Biology, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
Proc Natl Acad Sci U S A 107:4949-54. 2010
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- Executioner caspase-3 and caspase-7 are functionally distinct proteases
John G Walsh
Molecular Cell Biology Laboratory, Department of Genetics, The Smurfit Institute, Trinity College, Dublin 2, Ireland
Proc Natl Acad Sci U S A 105:12815-9. 2008
..Our observations provide a molecular basis for the different phenotypes seen in mice lacking either caspase and indicate that these proteases occupy nonredundant roles within the cell death machinery...
- Structure and catalytic mechanism of the human histone methyltransferase SET7/9
Bing Xiao
Structural Biology Group, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
Nature 421:652-6. 2003
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- Proteomics discovery of metalloproteinase substrates in the cellular context by iTRAQ labeling reveals a diverse MMP-2 substrate degradome
Richard A Dean
Department of Oral Biological and Medical Sciences, 4 401 Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
Mol Cell Proteomics 6:611-23. 2007
..Hence this advance in degradomics cell-based screens for native protein substrates casts new light on the roles for proteases in cell function...
- The anaphase promoting complex/cyclosome: a machine designed to destroy
Jan Michael Peters
Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Austria
Nat Rev Mol Cell Biol 7:644-56. 2006
..5-MDa complex. Recent discoveries have revealed an unexpected multitude of mechanisms that control APC/C activity, and have provided a first insight into how this unusual ubiquitin ligase recognizes its substrates...
- Crystal structure of glycogen synthase kinase 3 beta: structural basis for phosphate-primed substrate specificity and autoinhibition
R Dajani
Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, United Kingdom
Cell 105:721-32. 2001
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- Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases
Ankit Gupta
Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Nucleic Acids Res 39:381-92. 2011
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- A guanine nucleobase important for catalysis by the VS ribozyme
Timothy J Wilson
Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, UK
EMBO J 26:2489-500. 2007
..This is closely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for the two ribozymes appear topologically equivalent. This has probably arisen by convergent evolution...
- Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
Hao Bo Guo
Department of Biochemistry and Cellular and Molecular Biology, Center of Excellence in Structural Biology, University of Tennessee, Knoxville, TN 37996 0840, USA
Proc Natl Acad Sci U S A 104:8797-802. 2007
..The results of the simulations provide important insights into the catalytic process and lead to a better understanding of experimental observations concerning the origin of product specificity for PKMTs...
- Analysis of DHHC acyltransferases implies overlapping substrate specificity and a two-step reaction mechanism
Haitong Hou
University of Osnabruck, Department of Biology, Biochemistry Section, Osnabruck, Germany
Traffic 10:1061-73. 2009
..Here, we address the in vivo substrate specificity of five of the seven DHHC acyltransferases for peripheral membrane proteins by an overexpression approach...
- Basic and applied features of multicopper oxidases, CueO, bilirubin oxidase, and laccase
Takeshi Sakurai
Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920 1192, Japan
Chem Rec 7:220-9. 2007
..The substrate specificity of MCO for organic substrates is produced by the integrated effects of the shape of the substrate-binding ..
- Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts
Bjorn Rydberg
Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 99:16654-9. 2002
..Conversely, a highly purified archaeal RNase HII type 2 protein has a pronounced activity. To study substrate specificity, extracts were made from a yeast double mutant lacking the other main RNase H enzymes [RNase H1 and RNase ..
- Identification and characterization of an acyl-CoA:diacylglycerol acyltransferase 2 (DGAT2) gene from the microalga O. tauri
Martin Wagner
Department of Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences, Georg August University Gottingen, Gottingen, Germany
Plant Physiol Biochem 48:407-16. 2010
..Lipid analysis of the mutant yeast cells revealed that OtDGAT2B showed broad substrate specificity accepting saturated as well as mono- and poly-unsaturated acyl-CoAs as substrates.
- Fatty acyl-CoA reductase and wax synthase from Euglena gracilis in the biosynthesis of medium-chain wax esters
Prapapan Teerawanichpan
Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
Lipids 45:263-73. 2010
..These results indicate EgFAR and EgWS are likely the two enzymes involved in the biosynthesis of medium-chain wax esters in E. gracilis...
- Sequence-specific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates
Kvido Strisovsky
MRC Laboratory of Molecular Biology, Cambridge, UK
Mol Cell 36:1048-59. 2009
..Our work demonstrates that intramembrane proteases can be sequence specific and that genome-wide substrate prediction based on their recognition motifs is feasible...
- The wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase from Acinetobacter sp. strain ADP1: characterization of a novel type of acyltransferase
Tim Stöveken
Institut fur Molekulare Mikrobiologie und Biotechnologie, Westfalische Wilhelms Universitat Munster, Corrensstr 3, D 48149 Munster, Germany
J Bacteriol 187:1369-76. 2005
..Purified WS/DGAT revealed a remarkably low substrate specificity, accepting a broad range of various substances as alternative acceptor molecules...
- Substrate specificity of family 5, 6, 7, 9, 12, and 45 endoglucanases
E Vlasenko
Novozymes Inc, Davis, CA 95618, USA
Bioresour Technol 101:2405-11. 2010
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- Excision of oxidatively damaged DNA bases by the human alpha-hOgg1 protein and the polymorphic alpha-hOgg1(Ser326Cys) protein which is frequently found in human populations
C Dherin
CEA, DSV, DRR, UMR217 CNRS CEA, Radiobiologie Moléculaire et Cellulaire, Fontenay aux Roses, France
Nucleic Acids Res 27:4001-7. 1999
We have investigated the substrate specificity of the major nuclear form of the human Ogg1 protein, referred as alpha-hOgg1, for excision of damaged bases from DNA exposed to gamma-irradiation...
- Cuticular wax biosynthesis in petunia petals: cloning and characterization of an alcohol-acyltransferase that synthesizes wax-esters
Andrew King
Donald Danforth Plant Science Center, 975 N Warson Road, St Louis, MO 63132, USA
Planta 226:381-94. 2007
..In fact, the activity would be sufficient to produce most of the low molecular wax-esters present in petals, with methyl-esters being the exception. This work is the first characterization of a eukaryotic protein from the WS/DGAT family...
- Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases
P Lucas
Centre de Recherche sur la Fonction, , , , , , Canada
Nucleic Acids Res 29:960-9. 2001
..The high sequence variability we observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into how these proteins evolve new DNA specificity...
- Anchoring of surface proteins to the cell wall of Staphylococcus aureus. III. Lipid II is an in vivo peptidoglycan substrate for sortase-catalyzed surface protein anchoring
Adrienne M Perry
Committee on Microbiology, University of Chicago, Chicago, Illinois 60637, USA
J Biol Chem 277:16241-8. 2002
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- Identification of two novel human acyl-CoA wax alcohol acyltransferases: members of the diacylglycerol acyltransferase 2 (DGAT2) gene superfamily
Aaron R Turkish
Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
J Biol Chem 280:14755-64. 2005
..In situ hybridizations demonstrate a differentiation-specific expression pattern within the human sebaceous gland for the two AWAT genes, consistent with a significant role in the composition of sebum...
- Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds
Sylvestre Grizot
Cellectis SA, 102 Avenue Gaston Roussel, 93235 Romainville Cedex, France
Nucleic Acids Res 38:2006-18. 2010
..The DmoCre based meganucleases can therefore offer new possibilities for various genome engineering applications...
- Evolution of quaternary structure in a homotetrameric enzyme
Michael D W Griffin
School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
J Mol Biol 380:691-703. 2008
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- Mechanism of human SIRT1 activation by resveratrol
Margie T Borra
Department of Biomolecular Chemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
J Biol Chem 280:17187-95. 2005
..We propose that binding of resveratrol to SIRT1 promotes a conformational change that better accommodates the attached coumarin group...
- Legionella pneumophila glucosyltransferase inhibits host elongation factor 1A
Yury Belyi
Gamaleya Research Institute, Ulitsa Gamalei 18, Moscow 123098, Russia
Proc Natl Acad Sci U S A 103:16953-8. 2006
..Our findings show a mode of inhibition of protein synthesis by microbial pathogens and offer a perspective for understanding of the host-pathogen interaction of L. pneumophila...
- A genomic and functional inventory of deubiquitinating enzymes
Sebastian M B Nijman
Division of Molecular Carcinogenesis and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
Cell 123:773-86. 2005
..In addition, we review the literature concerning these enzymes, with particular emphasis on their function, specificity, and the regulation of their activity...
- Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity
Hui Wang
Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, PR China
EMBO J 29:2566-76. 2010
..the nuclease domain of CNOT6L exhibits full Mg(2+)-dependent deadenylase activity with strict poly(A) RNA substrate specificity. To understand the structural basis for poly(A) RNA substrate binding, crystal structures of the CNOT6L ..
- Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria
Robert Szczesny
Institut fur Biologie, Bereich Genetik, Martin Luther Universitat Halle Wittenberg, D 06099 Halle Saale, Germany
New Phytol 187:983-1002. 2010
..By contrast, expression of xynC and extracellular protease and xylanase activities are repressed by HrpG and HrpX, suggesting that components and substrates of the Xps system are differentially regulated...
- Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae
B Regenberg
Department of Yeast Genetics, Carlsberg Laboratory, Copenhagen Valby, Denmark
Curr Genet 36:317-28. 1999
..one or more of the 20 common L-alpha-amino acids was studied in order to obtain a complete picture of the substrate specificity for these permeases...
- Taking the plunge: integrating structural, enzymatic and computational insights into a unified model for membrane-immersed rhomboid proteolysis
Sinisa Urban
Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Biochem J 425:501-12. 2010
..Although far from complete, studies with GlpG currently offer the best prospect for achieving a thorough and sophisticated understanding of a simplified intramembrane protease...
- The structural basis for catalysis and substrate specificity of a rhomboid protease
Kutti R Vinothkumar
MRC Laboratory of Molecular Biology, Cambridge, UK
EMBO J 29:3797-809. 2010
..of the oxyanion hole, and the S₁- and S₂'-binding subsites of GlpG, which are the key determinants of substrate specificity. The inhibitor-bound structure suggests that subtle structural change is sufficient for catalysis, as ..
- Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases
John R Horton
Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
Nat Struct Mol Biol 17:38-43. 2010
..The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage ..
- Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion
Jesse G Zalatan
Department of Chemistry, Stanford University, Beckman Center B400, Stanford, CA 94305, USA
J Mol Biol 384:1174-89. 2008
..These results establish a new mechanistic model for this prototypical bimetallo enzyme and demonstrate the power of a comparative approach for probing biochemical function...
- Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12
Tracey M Gloster
York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
J Biol Chem 282:19177-89. 2007
..The differential strategies for the accommodation of the side chains of xyloglucan presumably facilitate the action of these microbial hydrolases in milieus where diverse and differently substituted substrates may be encountered...
- Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes
Mohamed Lamkanfi
Department of Pathology and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
Mol Cell Proteomics 7:2350-63. 2008
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- Crystal structures of MEK1 binary and ternary complexes with nucleotides and inhibitors
Thierry O Fischmann
Schering Plough Research Institute, Kenilworth, New Jersey 07033, USA
Biochemistry 48:2661-74. 2009
..Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome...
- Structural insights into substrate traffic and inhibition in acetylcholinesterase
Jacques-Philippe Colletier
, Institut de Biologie Structurale (CEA/CNRS/UJF, Grenoble Cedex, France
EMBO J 25:2746-56. 2006
..At the higher concentration, substrate inhibition arises from prevention of exit of acetate due to binding of two substrate molecules within the active-site gorge...
- Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4
Ted M Lakowski
Division of Biomolecular and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T1Z3, Canada
Biochem J 421:253-61. 2009
..Although PRMT2 activity is substantially lower than PRMT1 in vitro, the fact that both enzymes selectively methylate histone H4 suggest that PRMT2, like PRMT1, may act as a transcription co-activator through this modification...
- Replication across template T/U by human DNA polymerase-iota
Rinku Jain
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
Structure 17:974-80. 2009
..We also show that dATP and dGTP insert differently opposite template T/U, and that the basis of selection of dGTP over dATP is a hydrogen bond between the N2 amino group of dGTP and Gln59 of Poliota...
- Docking domains and substrate-specificity determination for MAP kinases
A D Sharrocks
School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester, UK M13 9PT
Trends Biochem Sci 25:448-53. 2000
..Additional specificity determinants in the substrates serve to enhance the specificity of substrate phosphorylation by MAP kinases further...
- Two crystal structures of pneumococcal pilus sortase C provide novel insights into catalysis and substrate specificity
Fabrice Neiers
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
J Mol Biol 393:704-16. 2009
..site-directed mutagenesis of Thr(160) in SrtB to an arginine as in SrtC (Arg(160)) partially converted its substrate specificity into that of SrtC...
- Function and regulation of the mitochondrial sirtuin isoform Sirt5 in Mammalia
Melanie Gertz
Department of Physiological Chemistry, Ruhr University Bochum, Bochum, Germany
Biochim Biophys Acta 1804:1658-65. 2010
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- RING domains: master builders of molecular scaffolds?
K L Borden
Department of Physiology and Biophysics, Mt Sinai School of Medicine, New York, NY, 10029, USA
J Mol Biol 295:1103-12. 2000
..Here, new developments, in the context of previous results, are discussed in an attempt to establish a unifying theory for RING function...
- Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects
Lien B Lai
Department of Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
FEBS Lett 584:287-96. 2010
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- Characterization of the substrate specificity of a human 5-hydroxymethyluracil glycosylase activity
David Baker
Department of Biochemistry and Microbiology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
Chem Res Toxicol 15:33-9. 2002
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- Tung tree DGAT1 and DGAT2 have nonredundant functions in triacylglycerol biosynthesis and are localized to different subdomains of the endoplasmic reticulum
Jay M Shockey
U S Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 70124, USA
Plant Cell 18:2294-313. 2006
..These data suggest that DGAT1 and DGAT2 have nonredundant functions in plants and that the production of storage oils, including those containing unusual fatty acids, occurs in distinct ER subdomains...
- Outlook for cellulase improvement: screening and selection strategies
Y H Percival Zhang
Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Biotechnol Adv 24:452-81. 2006
..Herein, we hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface...
- Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli
Matthew D Zimmerman
Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
J Mol Biol 378:215-26. 2008
..This is the first proposed molecular mechanism for an HD-domain phosphohydrolase based directly on substrate-bound crystal structures...
- The caspase-1 digestome identifies the glycolysis pathway as a target during infection and septic shock
Wei Shao
Department of Biochemistry, Division of Critical Care, Centre for the Study of Host Resistance, McGill University, Montreal, Quebec, Canada
J Biol Chem 282:36321-9. 2007
..The systematic characterization of caspase-1 substrates identifies the glycolysis pathway as a caspase-1 target and provides new insights into its function during pyroptosis and septic shock...
- Structural evidence for the evolution of xyloglucanase activity from xyloglucan endo-transglycosylases: biological implications for cell wall metabolism
Martin J Baumann
School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
Plant Cell 19:1947-63. 2007
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- Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity
Stanley S Ng
Structural Genomics Consortium, Botnar Research Center, University of Oxford, Oxford OX3 7LD, UK
Nature 448:87-91. 2007
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- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Stefanie Donat
Universitat Wurzburg, Institut für Molekulare Infektionsbiologie, Wurzburg, Germany
J Bacteriol 191:4056-69. 2009
..The results of this study strongly indicate that PknB has a role in regulation of purine biosynthesis, autolysis, and central metabolic processes in S. aureus...
- Regulation of ROS signal transduction by NADPH oxidase 4 localization
Kai Chen
Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
J Cell Biol 181:1129-39. 2008
..These data indicate that the specificity of intracellular ROS-mediated signal transduction may be modulated by the localization of Nox isoforms within specific subcellular compartments...
- Structural basis for the substrate specificity of tobacco etch virus protease
Jason Phan
Macromolecular Crystallography Laboratory, Center for Cancer Research, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702-1201, USA
J Biol Chem 277:50564-72. 2002
..Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological ..
- Engineering variants of the I-SceI homing endonuclease with strand-specific and site-specific DNA-nicking activity
Yan Niu
Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
J Mol Biol 382:188-202. 2008
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- The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution
Jason K Yano
Department of Molecular and Experimental Medicine and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
J Biol Chem 279:38091-4. 2004
..The structure of P450 3A4 should facilitate a better understanding of the substrate selectivity of the enzyme...
- Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase
Jean Francois Couture
Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109 0606, USA
Nat Struct Mol Biol 14:689-95. 2007
..We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs...
- Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function
Antti M Haapalainen
Biocenter Oulu and Department of Biochemistry, University of Oulu, P O Box 3000, FIN 90014 Oulu, Finland
Biochemistry 46:4305-21. 2007
..The structural analysis of the active site of T2 indicates that the Phe325-Pro326 dipeptide near the catalytic cavity is responsible for the exclusive 2-methyl-branched substrate specificity.
- Docking-based substrate recognition by the catalytic domain of a protein tyrosine kinase, C-terminal Src kinase (Csk)
Sungsoo Lee
Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island 02881, USA
J Biol Chem 281:8183-9. 2006
Protein tyrosine kinases are key enzymes of mammalian signal transduction. Substrate specificity is a fundamental property that determines the specificity and fidelity of signaling by protein tyrosine kinases...
- Unique substrate recognition by botulinum neurotoxins serotypes A and E
Sheng Chen
Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
J Biol Chem 281:10906-11. 2006
..These studies provide insight into the development of strategies for small molecule inhibitors of the BoNTs...
- Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering
Dorothée M Heckmann-Pohl
Institut fur Angewandte Mikrobiologie, Universitat des Saarlandes, Saarbrucken, Germany
J Biotechnol 124:26-40. 2006
..P2OxA and the analysis of the protein-ligand interactions in the docked complexes enabled us to explain the substrate specificity of the enzyme by a conserved hydrogen bond pattern which is formed between the protein and all substrates.
