- 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...
- Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
J Biol Chem 286:35334-8. 2011
- 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...
- 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...
- 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...
- Mammalian caspases: structure, activation, substrates, and functions during apoptosis
W C Earnshaw
Institute of Cell and Molecular Biology, University of Edinburgh, Scotland, United Kingdom
Annu Rev Biochem 68:383-424. 1999
..Collectively, these scissions disrupt survival pathways and disassemble important architectural components of the cell, contributing to the stereotypic morphological and biochemical changes that characterize apoptotic cell death...
- The conformational plasticity of protein kinases
Department of Biological Sciences, Stanford University, Palo Alto, California 94305, USA
Cell 109:275-82. 2002
..By contrast, crystal structures of inactive kinases have revealed a remarkable plasticity in the kinase domain that allows the adoption of distinct conformations in response to interactions with specific regulatory domains or proteins...
- 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?..
- 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...
- LKB1 is a master kinase that activates 13 kinases of the AMPK subfamily, including MARK/PAR-1
Jose M Lizcano
MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
EMBO J 23:833-43. 2004
..Between them, these kinases may mediate the physiological effects of LKB1, including its tumour suppressor 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...
- 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
- 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...
- Serine protease mechanism and specificity
Department of Biochemistry, MS 009, Brandeis University, Waltham, Massachusetts 02454, USA
Chem Rev 102:4501-24. 2002
- The small GTP-binding protein rac regulates growth factor-induced membrane ruffling
A J Ridley
Institute for Cancer Research, Chester Beatty Laboratories, London, England
Cell 70:401-10. 1992
..We propose that rac and rho are essential components of signal transduction pathways linking growth factors to the organization of polymerized actin...
- 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
- Targeting cancer with small molecule kinase inhibitors
Dana Farber Cancer Institute, Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Rev Cancer 9:28-39. 2009
..This Review provides a broad overview of some of the approaches currently used to discover and characterize new kinase inhibitors...
- 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...
- From promiscuity to precision: protein phosphatases get a makeover
David M Virshup
Program in Cancer and Stem Cell Biology, Duke NUS Graduate Medical School Singapore, Singapore, Republic of Singapore
Mol Cell 33:537-45. 2009
..As recent publications illustrate, these regulatory subunits confer specificity, selectivity, localization, and regulation on these important enzymes...
- 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...
- Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9
M H Tatham
Institute of Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews KY16 5ST, United Kingdom
J Biol Chem 276:35368-74. 2001
..The ability to form polymeric chains is not shared by SUMO-1, and although all SUMO species use the same conjugation machinery, modification by SUMO-1 and SUMO-2/-3 may have distinct functional consequences...
- 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...
- Multimodal activation of the ubiquitin ligase SCF by Nedd8 conjugation
Howard Hughes Medical Institute, Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
Mol Cell 32:21-31. 2008
- 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
- 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...
- MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis
Department of Biochemistry, Faculty of Medicine, Kyushu University, Fukuoka, Japan
Nature 355:273-5. 1992
..This indicates that elimination from the nucleotide pool of the oxidized form of guanine nucleotide is important for the high fidelity of DNA synthesis...
- One-thousand-and-one substrates of protein kinase CK2?
Dipartimento di Chimica Biologica and Istituto di Neuroscienze del CNR, Università di Padova and Venetian Institute for Molecular Medicine VIMM, Padova, Italy
FASEB J 17:349-68. 2003
..The possibility that CK2 phosphosites play some global role, e.g., by destabilizing alpha helices, counteracting caspase cleavage, and generating adhesive motifs, will be discussed...
- 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...
- How do site-specific DNA-binding proteins find their targets?
Stephen E Halford
Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
Nucleic Acids Res 32:3040-52. 2004
..Finally, we discuss how single molecule techniques might be used to study the dynamics of DNA site-specific targeting of proteins...
- 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...
- Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
Cell 121:1005-16. 2005
..In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism...
- 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.
- 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...
- Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks
Stacey M Southall
Institute of Cancer Research, Chester Beatty Laboratories, Chelsea, London, UK
Mol Cell 33:181-91. 2009
- 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...
- MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli
Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
Mol Cell 12:913-23. 2003
..The role of such endoribonucleases may have broad implication in cell physiology under various growth conditions...
- Ubiquitin: structures, functions, mechanisms
Cecile M Pickart
Department of Biochemistry and Molecular Biology Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
Biochim Biophys Acta 1695:55-72. 2004
..This article reviews the basic biochemistry of these protein conjugation reactions, focusing on ubiquitin itself and emphasizing recent insights into mechanism and specificity...
- Ribonuclease H: the enzymes in eukaryotes
Susana M Cerritelli
Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
FEBS J 276:1494-505. 2009
..Mutations in any of the three subunits of human RNase H2 cause Aicardi-Goutières syndrome, a human neurological disorder with devastating consequences...
- 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...
- The calpain system
Darrell E Goll
Muscle Biology Group, University of Arizona, Tucson, AZ 85721, USA
Physiol Rev 83:731-801. 2003
..Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma...
- Mus81-Eme1 are essential components of a Holliday junction resolvase
M N Boddy
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Cell 107:537-48. 2001
..The mus81 meiotic defect is rescued by expression of a bacterial Holliday junction resolvase. These findings constitute strong evidence that Mus81 and Eme1 are subunits of a nuclear Holliday junction resolvase...
- Mechanism of Holliday junction resolution by the human GEN1 protein
London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Herts, United Kingdom
Genes Dev 24:1559-69. 2010
..However, the unique feature of GEN1 that distinguishes it from other Rad2/XPG nucleases is its ability to dimerize on HJs. This functional adaptation provides the two symmetrically aligned active sites required for HJ resolution...
- Dicer recognizes the 5' end of RNA for efficient and accurate processing
Jong Eun Park
School of Biological Sciences, Seoul National University, Seoul 151 742, Korea
Nature 475:201-5. 2011
..Thus, 5'-end recognition by Dicer is important for precise and effective biogenesis of miRNAs. Insights from this study should also afford practical benefits to the design of small hairpin RNAs...
- The 1.6 Å crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate
Tien Chye Tan
School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
PLoS ONE 8:e53567. 2013
..of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity...
- A dynamic role of HAUSP in the p53-Mdm2 pathway
Institute for Cancer Genetics and Department of Pathology, College of Physicians and Surgeons, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
Mol Cell 13:879-86. 2004
..This study provides an example of an ubiquitin ligase (Mdm2) that is directly regulated by a deubiquitinase (HAUSP) and also reveals a dynamic role of HAUSP in the p53-Mdm2 pathway...
- ERK and p38 MAPK-activated protein kinases: a family of protein kinases with diverse biological functions
Philippe P Roux
Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
Microbiol Mol Biol Rev 68:320-44. 2004
..In this article, we review the existing data on the MKs and discuss their physiological functions based on recent discoveries...
- Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays
Programs in Cell Biology and Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
Mol Syst Biol 5:333. 2009
..relatives: Nedd4 (Nedd4-1) and Nedd4L (Nedd4-2), but their global substrate recognition or differences in substrate specificity are unknown...
- 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
- 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...
- Chaperone release and unfolding of substrates in type III secretion
Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA
Nature 437:911-5. 2005
..Our results show a similarity between the mechanisms of substrate recognition by type III protein secretion systems and AAA + ATPase disassembly machines...
- Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP
Division of Molecular Microbiology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
J Biol Chem 280:30829-37. 2005
- Crystal structure of the FTO protein reveals basis for its substrate specificity
National Institute of Biological Sciences, No 7 Science Park Road, Beijing 102206, China
Nature 464:1205-9. 2010
..Taken together, these results provide a structural basis for understanding FTO substrate-specificity, and serve as a foundation for the rational design of FTO inhibitors...
- Structure and functions of the GNAT superfamily of acetyltransferases
Matthew W Vetting
Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
Arch Biochem Biophys 433:212-26. 2005
- An overview of mannan structure and mannan-degrading enzyme systems
L R S Moreira
Departamento de Biologia Celular, Laboratorio De Enzimologia, Universidade de Brasilia, CEP 70910 900 Brasilia, DF, Brazil
Appl Microbiol Biotechnol 79:165-78. 2008
..Mannan-degrading enzymes have found applications in the pharmaceutical, food, feed, and pulp and paper industries. This review reports the structure of mannans and some biochemical properties and applications of mannan-degrading enzymes...
- 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...
- 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...
- 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...
- The Bloom's and Werner's syndrome proteins are DNA structure-specific helicases
Imperial Cancer Research Fund Laboratories, University of Oxford, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
Nucleic Acids Res 29:2843-9. 2001
..We interpret these data in the light of the genomic instability and hyper-recombination characteristics of cells from individuals with Bloom's or Werner's syndrome...
- A cytokine-responsive IkappaB kinase that activates the transcription factor NF-kappaB
J A DiDonato
Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, University of California at San Diego, La Jolla 92093 0636, USA
Nature 388:548-54. 1997
..A component of IKK was molecularly cloned and identified as a serine kinase. IKK turns out to be the long-sought-after protein kinase that mediates the critical regulatory step in NF-kappaB activation...
- Structural basis of RNA recognition and activation by innate immune receptor RIG-I
Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane West, Piscataway, New Jersey 08854, USA
Nature 479:423-7. 2011
..The structure yields unprecedented insight into innate immunity and has a broader impact on other areas of biology, including RNA interference and DNA repair, which utilize homologous helicase domains within DICER and FANCM...
- Oxidoreductive cellulose depolymerization by the enzymes cellobiose dehydrogenase and glycoside hydrolase 61
James A Langston
Novozymes, Inc, 1445 Drew Avenue, Davis, California 95618, USA
Appl Environ Microbiol 77:7007-15. 2011
..The action of GH61 and CDH on cellulose may constitute an important, but overlooked, biological oxidoreductive system that functions in microbial lignocellulose degradation and has applications in industrial biomass utilization...
- Comprehensive identification of protein substrates of the Dot/Icm type IV transporter of Legionella pneumophila
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
PLoS ONE 6:e17638. 2011
..Thus, our efforts have identified a large number of novel substrates of the Dot/Icm system and have revealed the diverse features recognizable by this protein transporter...
- Diversity in the serine recombinases
Margaret C M Smith
Institute of Genetics, Queens Medical Centre, University of Nottingham, NG7 2UH, UK
Mol Microbiol 44:299-307. 2002
..These observations indicate that the serine recombinases are modular and that fusion of the catalytic domain to unrelated sequences has generated structural and functional diversity...
- Small ubiquitin-related modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENPs
Program in Apoptosis and Cell Death Research, Burnham Institute for Medical Research, La Jolla, California 92037, USA
J Biol Chem 282:26217-24. 2007
..Using these synthetic substrates we reveal that the SUMO domain enhances catalysis of SENP1, -2, -5, -6, and -7, demonstrating substrate-induced activation of SENPs by SUMOs...
- MDR1 P-glycoprotein is a lipid translocase of broad specificity, while MDR3 P-glycoprotein specifically translocates phosphatidylcholine
A van Helvoort
Department of Cell Biology, Faculty of Medicine and Institute of Biomembranes, Universiteit Utrecht, The Netherlands
Cell 87:507-17. 1996
..Since no vesicular secretion occurs at 15 degrees C, the short-chain lipids must have been translocated by the Pgps across the plasma membrane before extraction into the medium by the lipid-acceptor albumin...
- 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.
- 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...
- Divergence and convergence in enzyme evolution: parallel evolution of paraoxonases from quorum-quenching lactonases
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
J Biol Chem 287:11-20. 2012
- The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes
M J Bessman
Department of Biology and The McCollum Pratt Institute, The Johns Hopkins University, Baltimore, Maryland 21218, USA
J Biol Chem 271:25059-62. 1996
- CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast
Department of Medical Genetics and Microbiology, University of Toronto, 1 King s College Circle, Toronto, M5S 1A8, Canada
Cell 117:899-913. 2004
..Elimination of CDK activity at the end of mitosis allows Whi5 to reenter the nucleus to again repress G1/S transcription. These findings harmonize G1/S control in eukaryotes...
- 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...
- What makes an enzyme promiscuous?
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
Curr Opin Chem Biol 14:200-7. 2010
- 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
- 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...
- 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...
- 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...
- Structural and sequence-based classification of glycoside hydrolases
Centre de Recherches sur les Macromolecules Vegetales, CNRS, Joseph Fourier Université, Grenoble, France
Curr Opin Struct Biol 7:637-44. 1997
..The recent analysis of these families, coupled with the burgeoning number of 3D structures, provides a detailed insight into the structure, function and catalytic mechanism of these enzymes...
- Regulation of AKT phosphorylation at Ser473 and Thr308 by endoplasmic reticulum stress modulates substrate specificity in a severity dependent manner
Hong Wa Yung
Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
PLoS ONE 6:e17894. 2011
..Here, we demonstrate that ER stress modulates AKT substrate specificity in a severity-dependent manner, as shown by phospho-specific antibodies against known AKT targets...
- 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...
- 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 ..
- 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
- 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
- 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...
- 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...
- 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 ..
- Mechanism of substrate selection by a highly specific CRISPR endoribonuclease
Samuel H Sternberg
Department of Chemistry, University of California, Berkeley, California 94720, USA
RNA 18:661-72. 2012
..b>Substrate specificity is achieved by RNA major groove contacts that are highly sensitive to helical geometry, as well as a ..
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Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
Nat Biotechnol 30:1232-9. 2012
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Charite Medical School, Institute of Virology CBF, Berlin, Germany
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Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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