- REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
Richard 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...
- SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity
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...
- 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...
- Genome engineering with zinc-finger nucleases
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112 5650, USA
Genetics 188:773-82. 2011
..The bright prospects for future applications of ZFNs, including human gene therapy, are discussed...
- A "silent" polymorphism in the MDR1 gene changes substrate specificity
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
Science 315:525-8. 2007
- 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...
- Strategies for MMP inhibition in cancer: innovations for the post-trial era
Christopher Mark Overall
Department of Oral Biological and Medical Sciences, C I H R Group in Matrix Dynamics, University of British Columbia, V6T 1Z3, Canada
Nat Rev Cancer 2:657-72. 2002
..What are the different approaches that can be used to target MMPs, and which of these might lead to new therapeutic strategies for cancer?..
- Enzyme promiscuity: a mechanistic and evolutionary perspective
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Annu Rev Biochem 79:471-505. 2010
..Finally, we address the hypothesis that promiscuous enzymatic activities serve as evolutionary starting points and highlight the unique evolutionary features of promiscuous enzyme functions...
- 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...
- NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity
Applied Bioinformatics, Center for Bioinformatics, Department of Computer Science, University of Tubingen, Sand 14, 72076 Tubingen, Germany
Nucleic Acids Res 39:W362-7. 2011
..The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to ..
- Substrate-specific activation of sirtuins by resveratrol
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...
- RNA helicases at work: binding and rearranging
Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
Trends Biochem Sci 36:19-29. 2011
..This review outlines our current view on major structural and mechanistic themes of RNA helicase function, and on emerging physical models for cellular roles of these enzymes...
- Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
Liam J Holt
Departments of Physiology and Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
Science 325:1682-6. 2009
..The gain or loss of phosphorylation sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits...
- Highly efficient endogenous human gene correction using designed zinc-finger nucleases
Fyodor 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...
- N-terminal acetylation of cellular proteins creates specific degradation signals
Cheol 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
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Nucleic Acids Res 38:5601-8. 2010
- Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily
Susan E Tsutakawa
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Cell 145:198-211. 2011
..conserved motifs bind and open dsDNA; direct the target region into the helical gateway, permitting only nonbase-paired oligonucleotides active site access; and support a unified understanding of superfamily substrate specificity.
- Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast
Biochemistry Department, Weill Medical College of Cornell University, New York, New York 10021, USA
Mol Cell 5:865-76. 2000
..Genetic analysis guided by the structure further reveals a regulatory element N-terminal to the proteolytic domain that is required for cell growth in yeast...
- Tapping natural reservoirs of homing endonucleases for targeted gene modification
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North A3 025, Seattle, WA 98109, USA
Proc Natl Acad Sci U S A 108:13077-82. 2011
..The ubiquitous presence and diversity of LHEs described in this study may facilitate the creation of many tailored nucleases for genome editing...
- 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...
- Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery
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...
- Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
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...
- Structure of a Fbw7-Skp1-cyclin E complex: multisite-phosphorylated substrate recognition by SCF ubiquitin ligases
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Mol Cell 26:131-43. 2007
- Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs
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...
- SRT1720, SRT2183, SRT1460, and resveratrol are not direct activators of SIRT1
Department of Cardiovascular, Pfizer Global Research and Development, Groton, Connecticut 06340, USA
J Biol Chem 285:8340-51. 2010
..Taken together, we conclude that SRT1720, SRT2183, SRT1460, and resveratrol are not direct activators of SIRT1...
- Nucleotidyl cyclase activity of soluble guanylyl cyclase α1β1
Kerstin Y Beste
Institute of Pharmacology, Hannover Medical School, Hannover, Germany
Biochemistry 51:194-204. 2012
..In conclusion, soluble "guanylyl" cyclase possesses much broader substrate specificity than previously assumed...
- 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...
- 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...
- 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...
- Functions of site-specific histone acetylation and deacetylation
Mona D Shahbazian
Department of Biological Chemistry, Geffen School of Medicine and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
Annu Rev Biochem 76:75-100. 2007
..Determining how these enzymes create distinct acetylation patterns and regulate the functional outcome is an important challenge...
- Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase
Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
Mol Cell 11:1445-56. 2003
- 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...
- Enzyme promiscuity: evolutionary and mechanistic aspects
Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
Curr Opin Chem Biol 10:498-508. 2006
- What makes an enzyme promiscuous?
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
Curr Opin Chem Biol 14:200-7. 2010
- 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...
- 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...
- 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...
- HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues
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...
- Crystal structure of glycogen synthase kinase 3 beta: structural basis for phosphate-primed substrate specificity and autoinhibition
Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, United Kingdom
Cell 105:721-32. 2001
- The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases
N R Brown
Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
Nat Cell Biol 1:438-43. 1999
..These residues include the RXL motif required to target p107 to cyclins. This structure explains the specificity of the RXL motif for cyclins...
- DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected]
C D Mol
Skaggs Institute for Chemical Biology, and the Department of Molecular Biology, La Jolla, California 92037 1027, USA
Nature 403:451-6. 2000
- Acetylation: a regulatory modification to rival phosphorylation?
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.
- Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases
Institut fur Biochemie, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392, Giessen, Germany
Nucleic Acids Res 40:847-60. 2012
- Determination of protease cleavage site motifs using mixture-based oriented peptide libraries
B E Turk
Department of Medicine, Beth Israel Deaconess Medical Center, Department of Cell Biology, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
Nat Biotechnol 19:661-7. 2001
..Our results indicate that a small set of libraries can be used to quickly profile an expanding protease family, providing information applicable to the design of inhibitors and to the identification of protein substrates...
- Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts
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 ..
- Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
Center for Bioinformatics Tübingen ZBIT, University of Tubingen, Germany
Nucleic Acids Res 33:5799-808. 2005
We present a new support vector machine (SVM)-based approach to predict the substrate specificity of subtypes of a given protein sequence family...
- Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines
M H Kuo
Department of Biology, University of Rochester, New York 14627, USA
Nature 383:269-72. 1996
- Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
Nat Biotechnol 30:1232-9. 2012
- An unbiased genome-wide analysis of zinc-finger nuclease specificity
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
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
MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Nature 458:859-64. 2009
- Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations
R B Pearson
Methods Enzymol 200:62-81. 1991
- PMAP: databases for analyzing proteolytic events and pathways
The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Nucleic Acids Res 37:D611-8. 2009
..Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis...
- The yeast Pif1p helicase removes telomerase from telomeric DNA
Jean Baptiste Boulé
Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
Nature 438:57-61. 2005
..We propose that Pif1p helicase activity limits telomerase action both in vivo and in vitro by displacing active telomerase from DNA ends...
- 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...
- Design and evolution of new catalytic activity with an existing protein scaffold
Hee Sung Park
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373 1, Kusung dong, Yusung Gu, Daejon 305 701, Korea
Science 311:535-8. 2006
..8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100...
- Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae
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...
- Identification of a gene coding for a deglycosylating enzyme in Hypocrea jecorina
Department of Biochemistry and Microbiology, Faculty of Applied Engineering Sciences, Ghent University, Ghent, Belgium
FEMS Microbiol Lett 303:9-17. 2010
..This ENGase activity, not coregulated with cellulase production, could be responsible for the extensive N-deglycosylation observed for several T. reesei cellulases...
- A unique family of Mrr-like modification-dependent restriction endonucleases
New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
Nucleic Acids Res 38:5527-34. 2010
..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms...
- Unlocking the sugar "steric gate" of DNA polymerases
Jessica A Brown
Department of Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
Biochemistry 50:1135-42. 2011
..These important findings are summarized in this review...
- Selenocysteine lyase, a novel enzyme that specifically acts on selenocysteine. Mammalian distribution and purification and properties of pig liver enzyme
J Biol Chem 257:4386-91. 1982
..L-Cysteine (Ki, 1.0 mM) competes with L-selenocysteine (Km, 0.83 mM) to inhibit the enzyme reaction. The enzyme is the first proven enzyme that specifically acts on selenium compounds...
- A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily
Edwin van Bloois
Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
Appl Microbiol Biotechnol 86:1419-30. 2010
..In conclusion, the detailed biochemical characterization reported here contributes significantly to our understanding of these enzymes and further emphasizes their biotechnological potential...
- Ligand binding and substrate discrimination by UDP-galactopyranose mutase
Todd D Gruber
Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
J Mol Biol 391:327-40. 2009
..To understand the consequences of these differences, we derived a model for the productive UGM-substrate complex that highlights interactions that can contribute to catalysis and substrate discrimination...
- Phylogenetic analyses suggest multiple changes of substrate specificity within the glycosyl hydrolase 20 family
Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
BMC Evol Biol 8:214. 2008
..Nevertheless, only limited analyses of phylogenetic relationships between GH20 genes have been performed until now...
- Synthesis of novel lipids in Saccharomyces cerevisiae by heterologous expression of an unspecific bacterial acyltransferase
Institut fur Molekulare Mikrobiologie und Biotechnologie, Westfalische Wilhelms Universitat, Munster, 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...
- 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...
- 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...
- Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector
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...
- 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
- Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
Macromolecular Crystallography Group, Spanish National Cancer Research Centre CNIO, c Melchor Fdez Almagro 3, 28029 Madrid, Spain
Nature 456:107-11. 2008
- 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...
- Regulation of p53 activity through lysine methylation
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...
- Enzymatic action of prostate-specific antigen (PSA or hK3): substrate specificity and regulation by Zn(2+), a tight-binding inhibitor
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.
- 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...
- Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family
Systèmes moléculaires et Biologie structurale, LMCP, CNRS UMR 7590, Universités Paris 6 et Paris 7, case 115, 4 place Jussieu, F 75252 Paris Cedex 05, France
Nucleic Acids Res 30:3592-601. 2002
..and genome data also allowed us to unravel particular sequence features which are likely to be involved in substrate specificity, as well as to describe new but as yet uncharacterised members which may play critical roles in DNA and ..
- Coding of odors by a receptor repertoire
Elissa A Hallem
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Cell 125:143-60. 2006
..The space provides a basis for predicting behavioral responses to odors...
- Cracking the phosphatase code: docking interactions determine substrate specificity
Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305 5020, USA
Sci Signal 2:re9. 2009
Phosphoserine- and phosphothreonine-directed phosphatases display remarkable substrate specificity, yet the sites that they dephosphorylate show little similarity in amino acid sequence...
- 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...
- Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
Structure 11:509-20. 2003
..Three peptide binding channels are identified: two are between the two domains, and the third is on the surface perpendicular to the strands forming the beta barrel...
- Analysis of the DNA substrate specificity of the human BACH1 helicase associated with breast cancer
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...
- 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...
- 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
- Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)
Division of Glycoscience, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm SE 106 91, Sweden
BMC Evol Biol 12:186. 2012
..With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5...
- Human cyclic nucleotide phosphodiesterases possess a much broader substrate-specificity than previously appreciated
Institute of Pharmacology, Medical School of Hannover, Hannover, Germany
FEBS Lett 585:3259-62. 2011
..Using an HPLC-MS based assay, here, we show that human PDEs belonging to various families hydrolyze not only cAMP and cGMP but also other cyclic nucleotides...
- The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs
Institute of Molecular Cancer Research, University of Zurich, August Forel Strasse 7, Ch 8008 Zurich, Switzerland
Nucleic Acids Res 31:2261-71. 2003
- L-685,458, an aspartyl protease transition state mimic, is a potent inhibitor of amyloid beta-protein precursor gamma-secretase activity
M S Shearman
Department of Molecular Biology, Merck Sharp and Dohme Research Laboratories, The Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, England
Biochemistry 39:8698-704. 2000
..Specific and potent inhibitors of A beta PP gamma-secretase activity such as L-685,458 will enable important advances toward the identification and elucidation of the mechanism of action of this enigmatic protease...
- 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...
- Structure and catalytic mechanism of the human histone methyltransferase SET7/9
Structural Biology Group, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
Nature 421:652-6. 2003
- 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...
- Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases
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
- Cuticular wax biosynthesis in petunia petals: cloning and characterization of an alcohol-acyltransferase that synthesizes wax-esters
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...
- 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
- Basic and applied features of multicopper oxidases, CueO, bilirubin oxidase, and laccase
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 ..
- 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...
- Substrate specificity of family 5, 6, 7, 9, 12, and 45 endoglucanases
Novozymes Inc, Davis, CA 95618, USA
Bioresour Technol 101:2405-11. 2010
- The wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase from Acinetobacter sp. strain ADP1: characterization of a novel type of acyltransferase
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...
- Sequence-specific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates
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...
- 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...
- 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...