The Origins of Specificity in the Microcin-Processing Protease TldD/E
Tài liệu tham khảo
Allali, 2002, The highly conserved TldD and TldE proteins of Escherichia coli are involved in microcin B17 processing and in CcdA degradation, J. Bacteriol., 184, 3224, 10.1128/JB.184.12.3224-3231.2002
Arnison, 2013, Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature, Nat. Prod. Rep., 30, 108, 10.1039/C2NP20085F
Bahassi, 1999, Interactions of CcdB with DNA gyrase. Inactivation of Gyra, poisoning of the gyrase-DNA complex, and the antidote action of CcdA, J. Biol. Chem., 274, 10936, 10.1074/jbc.274.16.10936
Baral, 2008, The first structure of dipeptidyl-peptidase III provides insight into the catalytic mechanism and mode of substrate binding, J. Biol. Chem., 283, 22316, 10.1074/jbc.M803522200
Bernard, 1991, The 41 carboxy-terminal residues of the miniF plasmid CcdA protein are sufficient to antagonize the killer activity of the CcdB protein, Mol. Gen. Genet., 226, 297, 10.1007/BF00273616
Bertini, 2006, Snapshots of the reaction mechanism of matrix metalloproteinases, Angew. Chem. Int. Ed., 45, 7952, 10.1002/anie.200603100
Burger, 2017, Hidden states within disordered regions of the CcdA antitoxin protein, J. Am. Chem. Soc., 139, 2693, 10.1021/jacs.6b11450
Cerda-Costa, 2014, Architecture and function of metallopeptidase catalytic domains, Protein Sci., 23, 123, 10.1002/pro.2400
Chan, 1997, Crystal structure of the Escherichia coli peptide deformylase, Biochemistry, 36, 13904, 10.1021/bi9711543
Cowtan, 2006, The Buccaneer software for automated model building. 1. Tracing protein chains, Acta Crystallogr. D Biol. Crystallogr., 62, 1002, 10.1107/S0907444906022116
Cowtan, 2010, Recent developments in classical density modification, Acta Crystallogr. D Biol. Crystallogr., 66, 470, 10.1107/S090744490903947X
Datsenko, 2000, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc. Natl. Acad. Sci. USA, 97, 6640, 10.1073/pnas.120163297
Davis, 2007, MolProbity: all-atom contacts and structure validation for proteins and nucleic acids, Nucleic Acids Res., 35, W375, 10.1093/nar/gkm216
De Jonge, 2009, Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain, Mol. Cell, 35, 154, 10.1016/j.molcel.2009.05.025
Demeler, 2005, UltraScan: a comprehensive data analysis software package for analytical ultracentrifugation experiments, 201
Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158
Evans, 2013, How good are my data and what is the resolution?, Acta Crystallogr. D Biol. Crystallogr., 69, 1204, 10.1107/S0907444913000061
Garrido, 1988, The export of the DNA replication inhibitor Microcin B17 provides immunity for the host cell, EMBO J., 7, 1853, 10.1002/j.1460-2075.1988.tb03018.x
Genilloud, 1989, DNA sequence, products, and transcriptional pattern of the genes involved in production of the DNA replication inhibitor microcin B17, J. Bacteriol., 171, 1126, 10.1128/jb.171.2.1126-1135.1989
Ghilarov, 2011, A major portion of DNA gyrase inhibitor microcin B17 undergoes an N,O-peptidyl shift during synthesis, J. Biol. Chem., 286, 26308, 10.1074/jbc.M111.241315
Heddle, 2001, The antibiotic microcin B17 is a DNA gyrase poison: characterisation of the mode of inhibition, J. Mol. Biol., 307, 1223, 10.1006/jmbi.2001.4562
Holden, 1988, The binding of L-valyl-L-tryptophan to crystalline thermolysin illustrates the mode of interaction of a product of peptide hydrolysis, J. Biol. Chem., 263, 3256, 10.1016/S0021-9258(18)69064-7
Hu, 2012, An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease, Biosci. Rep., 32, 609, 10.1042/BSR20120074
Inouye, 2007, Engineering, expression, purification, and production of recombinant thermolysin, Biotechnol. Annu. Rev., 13, 43, 10.1016/S1387-2656(07)13003-9
Kabsch, 2010, Xds, Acta Crystallogr. D Biol. Crystallogr., 66, 125, 10.1107/S0907444909047337
Kelleher, 1999, Posttranslational heterocyclization of cysteine and serine residues in the antibiotic microcin B17: distributivity and directionality, Biochemistry, 38, 15623, 10.1021/bi9913698
Kleemann, 1986, Metal-binding to angiotensin converting enzyme - implications for the metal-binding site, J. Inorg. Biochem., 26, 93, 10.1016/0162-0134(86)80002-2
Krissinel, 2015, Stock-based detection of protein oligomeric states in jsPISA, Nucleic Acids Res., 43, W314, 10.1093/nar/gkv314
Krissinel, 2004, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallogr. D Biol. Crystallogr., 60, 2256, 10.1107/S0907444904026460
Lee, 2008, Discovery of a widely distributed toxin biosynthetic gene cluster, Proc. Natl. Acad. Sci. USA, 105, 5879, 10.1073/pnas.0801338105
Li, 1996, From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase, Science, 274, 1188, 10.1126/science.274.5290.1188
Maki, 1992, Modulation of DNA supercoiling activity of Escherichia coli DNA gyrase by F plasmid proteins. Antagonistic actions of LetA (CcdA) and LetD (CcdB) proteins, J. Biol. Chem., 267, 12244, 10.1016/S0021-9258(19)49831-1
Malito, 2008, Amyloid beta-degrading cryptidases: insulin degrading enzyme, presequence peptidase, and neprilysin, Cell. Mol. Life Sci., 65, 2574, 10.1007/s00018-008-8112-4
Massaoud, 2011, Enzymatic characterization of a serralysin-like metalloprotease from the entomopathogen bacterium, Xenorhabdus, Biochim. Biophys. Acta, 1814, 1333, 10.1016/j.bbapap.2011.05.008
Matthews, 1972, Three-dimensional structure of thermolysin, Nat. New Biol., 238, 37, 10.1038/newbio238037a0
Mayaux, 1982, Removal of the tightly bound zinc from Escherichia coli trypsin-modified methionyl-tRNA synthetase, Eur. J. Biochem., 128, 41, 10.1111/j.1432-1033.1982.tb06928.x
Mccoy, 2007, Phaser crystallographic software, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206
McNicholas, 2011, Presenting your structures: the CCP4mg molecular-graphics software, Acta Crystallogr. D Biol. Crystallogr., 67, 386, 10.1107/S0907444911007281
Metelev, 2013, Structure of microcin B-like compounds produced by Pseudomonas syringae and species specificity of their antibacterial action, J. Bacteriol., 195, 4129, 10.1128/JB.00665-13
Miki, 1984, Control of cell division by sex factor F in Escherichia coli. II. Identification of genes for inhibitor protein and trigger protein on the 42.84-43.6 F segment, J. Mol. Biol., 174, 627, 10.1016/0022-2836(84)90087-1
Murayama, 1996, Evidence for involvement of Escherichia coli genes pmbA, csrA and a previously unrecognized gene tldD, in the control of DNA gyrase by letD (ccdB) of sex factor F, J. Mol. Biol., 256, 483, 10.1006/jmbi.1996.0103
Murshudov, 1997, Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D Biol. Crystallogr., 53, 240, 10.1107/S0907444996012255
Painter, 2006, Optimal description of a protein structure in terms of multiple groups undergoing TLS motion, Acta Crystallogr. D Biol. Crystallogr., 62, 439, 10.1107/S0907444906005270
Rife, 2005, Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 Å resolution reveals a new fold, Proteins, 61, 444, 10.1002/prot.20468
Robert, 2014, Deciphering key features in protein structures with the new ENDscript server, Nucleic Acids Res., 42, W320, 10.1093/nar/gku316
Rodriguez-Sainz, 1990, Molecular characterization of pmbA, an Escherichia coli chromosomal gene required for the production of the antibiotic peptide MccB17, Mol. Microbiol., 4, 1921, 10.1111/j.1365-2958.1990.tb02041.x
Roy, 1999, Expressed protein ligation to probe regiospecificity of heterocyclization in the peptide antibiotic microcin B17, Chem. Biol., 6, 789, 10.1016/S1074-5521(99)80126-4
Roy, 1998, Role of the microcin B17 propeptide in substrate recognition: solution structure and mutational analysis of McbA1-26, Chem. Biol., 5, 217, 10.1016/S1074-5521(98)90635-4
Schechter, 1967, On the size of the active site in proteases. I. Papain, Biochem. Biophys. Res. Commun., 27, 157, 10.1016/S0006-291X(67)80055-X
Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75
Sinha Roy, 1999, In vivo processing and antibiotic activity of microcin B17 analogs with varying ring content and altered bisheterocyclic sites, Chem. Biol., 6, 305, 10.1016/S1074-5521(99)80076-3
Stein, 2008, CHAINSAW: a program for mutating pdb files used as templates in molecular replacement, J. Appl. Crystallogr., 41, 641, 10.1107/S0021889808006985
Tyndall, 2005, Proteases universally recognize beta strands in their active sites, Chem. Rev., 105, 973, 10.1021/cr040669e
Vallee, 1957, Zinc in horse liver alcohol dehydrogenase, J. Biol. Chem., 225, 185, 10.1016/S0021-9258(18)64921-X
Van Melderen, 1994, Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria, Mol. Microbiol., 11, 1151, 10.1111/j.1365-2958.1994.tb00391.x
Van Melderen, 1996, ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions, J. Biol. Chem., 271, 27730, 10.1074/jbc.271.44.27730
Waterhouse, 2009, Jalview Version 2-a multiple sequence alignment editor and analysis workbench, Bioinformatics, 25, 1189, 10.1093/bioinformatics/btp033
Winter, 2010, xia2: an expert system for macromolecular crystallography data reduction, J. Appl. Crystallogr., 43, 186, 10.1107/S0021889809045701
Xu, 2009, Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism, J. Am. Chem. Soc., 131, 9780, 10.1021/ja9027988