EzCatDB: D00510
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DB codeD00510
RLCP classification1.13.30100.19 : Hydrolysis
CATH domainDomain 12.10.109.10 : Umud Fragment, subunit ACatalytic domain
Domain 21.10.10.10 : Arc Repressor Mutant, subunit A
E.C.3.4.21.88
CSA1jhf

CATH domainRelated DB codes (homologues)
1.10.10.10 : Arc Repressor Mutant, subunit AD00452,D00077,D00517,T00055,T00113

Enzyme Name
UniProtKBKEGG

P0A7C2
Protein nameLexA repressorrepressor LexA
LexA repressor
SynonymsEC 3.4.21.88
RefSeqNP_418467.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492186.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
MEROPSS24.001 (Serine)
PfamPF01726 (LexA_DNA_bind)
PF00717 (Peptidase_S24)
[Graphical view]


UniProtKB:Accession NumberP0A7C2
Entry nameLEXA_ECOLI
ActivityHydrolysis of Ala-|-Gly bond in repressor lexA.
SubunitHomodimer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC99999C00001C00017C00012I00087I00085I00086
CompoundRepressor LexAH2OProteinPeptidePeptidyl-tetrahedral intermediateAcyl-enzymeTetrahedral intermediate
Typepeptide/proteinH2Opeptide/proteinpeptide/protein


ChEBI
15377





PubChem
962
22247451





               
1jhcAUnbound UnboundUnbound   
1jheABound:ALA 84-GLY 85(chain A) UnboundUnbound   
1jheBBound:ALA 84-GLY 85(chain B) UnboundUnbound   
1jhfA01Unbound UnboundUnbound   
1jhfBUnbound UnboundUnbound   
1jhhA01Unbound UnboundUnbound   
1jhhBBound:ALA 84-GLY 85(chain B) UnboundUnbound   
1jhfA02Unbound UnboundUnbound   
1jhhA02Unbound UnboundUnbound   
1leaAUnbound UnboundUnbound   
1lebAUnbound UnboundUnbound   

Active-site residues
resource
literature [4], [8], [13], [28]
pdbCatalytic residuesMain-chain involved in catalysiscomment
           
1jhcA       ;LYS 156
MET 118;       
mutant S119A
1jheASER 119;       
MET 118;SER 119
mutant L89P, Q92W, E152A, K156A
1jheBSER 119;       
MET 118;SER 119
mutant L89P, Q92W, E152A, K156A
1jhfA01SER 119;LYS 156
MET 118;SER 119
mutant G85D
1jhfBSER 119;LYS 156
MET 118;SER 119
 
1jhhA01       ;LYS 156
MET 118;       
mutant S119A
1jhhB       ;LYS 156
MET 118;       
mutant S119A
1jhfA02 
 
 
1jhhA02 
 
 
1leaA 
 
 
1lebA 
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Fig.4, p.3990-3991
[8]Fig.1, p.12834-12835
[10]Fig.2, p.416-417
[13]p.921-922
[28]p.588-589

references
[1]
CommentsFUNCTION.
Medline ID82037807
PubMed ID7027256
JournalProc Natl Acad Sci U S A
Year1981
Volume78
Pages4204-8
AuthorsBrent R, Ptashne M
TitleMechanism of action of the lexA gene product.
Related UniProtKBP0A7C2
[2]
CommentsFUNCTION.
Medline ID82037806
PubMed ID7027255
JournalProc Natl Acad Sci U S A
Year1981
Volume78
Pages4199-203
AuthorsLittle JW, Mount DW, Yanisch-Perron CR
TitlePurified lexA protein is a repressor of the recA and lexA genes.
Related UniProtKBP0A7C2
[3]
PubMed ID3709524
JournalEMBO J
Year1986
Volume5
Pages793-8
AuthorsHurstel S, Granger-Schnarr M, Daune M, Schnarr M
TitleIn vitro binding of LexA repressor to DNA: evidence for the involvement of the amino-terminal domain.
[4]
PubMed ID3108885
JournalProc Natl Acad Sci U S A
Year1987
Volume84
Pages3987-91
AuthorsSlilaty SN, Little JW
TitleLysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism.
[5]
PubMed ID2834329
JournalJ Bacteriol
Year1988
Volume170
Pages2163-73
AuthorsLin LL, Little JW
TitleIsolation and characterization of noncleavable (Ind-) mutants of the LexA repressor of Escherichia coli K-12.
[6]
CommentsSTRUCTURE BY NMR.
Medline ID89386639
PubMed ID2780544
JournalProc Natl Acad Sci U S A
Year1989
Volume86
Pages6863-7
AuthorsLamerichs RM, Padilla A, Boelens R, Kaptein R, Ottleben G, Ruterjans H, Granger-Schnarr M, Oertel P, Schnarr M
TitleThe amino-terminal domain of LexA repressor is alpha-helical but differs from canonical helix-turn-helix proteins: a two-dimensional 1H NMR study.
Related UniProtKBP0A7C2
[7]
PubMed ID2184894
JournalBiochemistry
Year1990
Volume29
Pages1961-70
AuthorsHurstel S, Granger-Schnarr M, Schnarr M
TitleThe LexA repressor and its isolated amino-terminal domain interact cooperatively with poly[d(A-T)], a contiguous pseudo-operator, but not with random DNA: a circular dichroism study.
[8]
PubMed ID2198279
JournalJ Biol Chem
Year1990
Volume265
Pages12828-35
AuthorsRoland KL, Little JW
TitleReaction of LexA repressor with diisopropyl fluorophosphate. A test of the serine protease model.
[9]
PubMed ID2259342
JournalMol Gen Genet
Year1990
Volume223
Pages40-8
AuthorsOertel-Buchheit P, Lamerichs RM, Schnarr M, Granger-Schnarr M
TitleGenetic analysis of the LexA repressor: isolation and characterization of LexA(Def) mutant proteins.
[10]
PubMed ID1911941
JournalBiochimie
Year1991
Volume73
Pages411-21
AuthorsLittle JW
TitleMechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease.
[11]
PubMed ID1911942
JournalBiochimie
Year1991
Volume73
Pages423-31
AuthorsSchnarr M, Oertel-Buchheit P, Kazmaier M, Granger-Schnarr M
TitleDNA binding properties of the LexA repressor.
[12]
PubMed ID1815638
JournalJ Biomol Struct Dyn
Year1991
Volume9
Pages447-61
AuthorsOttleben G, Messori L, Ruterjans H, Kaptein R, Granger-Schnarr M, Schnarr M
Title1H-NMR investigation of the interaction of the amino terminal domain of the LexA repressor with a synthetic half-operator.
[13]
PubMed ID1667880
JournalProtein Eng
Year1991
Volume4
Pages919-22
AuthorsSlilaty SN, Vu HK
TitleThe role of electrostatic interactions in the mechanism of peptide bond hydrolysis by a Ser-Lys catalytic dyad.
[14]
PubMed ID1602473
JournalJ Mol Biol
Year1992
Volume225
Pages609-20
AuthorsOertel-Buchheit P, Porte D, Schnarr M, Granger-Schnarr M
TitleIsolation and characterization of LexA mutant repressors with enhanced DNA binding affinity.
[15]
PubMed ID1453451
JournalJ Mol Biol
Year1992
Volume228
Pages395-408
AuthorsRoland KL, Smith MH, Rupley JA, Little JW
TitleIn vitro analysis of mutant LexA proteins with an increased rate of specific cleavage.
[16]
PubMed ID1620111
JournalMol Cell Biol
Year1992
Volume12
Pages3006-14
AuthorsGolemis EA, Brent R
TitleFused protein domains inhibit DNA binding by LexA.
[17]
PubMed ID8513500
JournalCell
Year1993
Volume73
Pages1165-73
AuthorsKim B, Little JW
TitleLexA and lambda Cl repressors as enzymes: specific cleavage in an intermolecular reaction.
[18]
PubMed ID8349538
JournalJ Bacteriol
Year1993
Volume175
Pages4943-50
AuthorsLittle JW
TitleLexA cleavage and other self-processing reactions.
[19]
CommentsSTRUCTURE BY NMR.
Medline ID94357165
PubMed ID8076591
JournalEMBO J
Year1994
Volume13
Pages3936-44
AuthorsFogh RH, Ottleben G, Ruterjans H, Schnarr M, Boelens R, Kaptein R
TitleSolution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy.
Related PDB1lea,1leb
Related UniProtKBP0A7C2
[20]
PubMed ID7716155
JournalProtein Eng
Year1994
Volume7
Pages1449-53
AuthorsHolm L, Sander C, Ruterjans H, Schnarr M, Fogh R, Boelens R, Kaptein R
TitleLexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily.
[21]
Comments3D-STRUCTURE MODELING.
Medline ID95303877
PubMed ID7784426
JournalProteins
Year1995
Volume21
Pages226-36
AuthorsKnegtel RM, Fogh RH, Ottleben G, Ruterjans H, Dumoulin P, Schnarr M, Boelens R, Kaptein R
TitleA model for the LexA repressor DNA complex.
Related UniProtKBP0A7C2
[22]
PubMed ID8605176
JournalBiochemistry
Year1996
Volume35
Pages4279-86
AuthorsDumoulin P, Ebright RH, Knegtel R, Kaptein R, Granger-Schnarr M, Schnarr M
TitleStructure of the LexA repressor-DNA complex probed by affinity cleavage and affinity photo-cross-linking.
[23]
PubMed ID8876169
JournalProc Natl Acad Sci U S A
Year1996
Volume93
Pages11528-33
AuthorsShepley DP, Little JW
TitleMutant LexA proteins with specific defects in autodigestion.
[24]
PubMed ID9512712
JournalJ Mol Biol
Year1998
Volume276
Pages405-15
AuthorsKonola JT, Guzzo A, Gow JB, Walker GC, Knight KL
TitleDifferential cleavage of LexA and UmuD mediated by recA Pro67 mutants: implications for common LexA and UmuD binding sites on RecA.
[25]
PubMed ID9521130
JournalProtein Sci
Year1998
Volume7
Pages512-5
AuthorsOertel-Buchheit P, Reinbolt J, John M, Granger-Schnarr M, Schnarr M
TitleA LexA mutant repressor with a relaxed inter-domain linker.
[26]
PubMed ID10692372
JournalJ Bacteriol
Year2000
Volume182
Pages1659-70
AuthorsMustard JA, Little JW
TitleAnalysis of Escherichia coli RecA interactions with LexA, lambda CI, and UmuD by site-directed mutagenesis of recA.
[27]
CommentsModel
PubMed ID11089640
JournalJ Biomol Struct Dyn
Year2000
Volume18
Pages181-97
AuthorsChattopadhyaya R, Ghosh K, Namboodiri VM
TitleModel of a LexA repressor dimer bound to recA operator.
Related PDB1qaa
[28]
CommentsX-RAY DIFFRACTION
PubMed ID11551506
JournalCell
Year2001
Volume106
Pages585-94
AuthorsLuo Y, Pfuetzner RA, Mosimann S, Paetzel M, Frey EA, Cherney M, Kim B, Little JW, Strynadka NC
TitleCrystal structure of LexA: a conformational switch for regulation of self-cleavage.
Related PDB1jhc,1jhe,1jhf,1jhh
[29]
PubMed ID11583611
JournalMol Cell
Year2001
Volume8
Pages486-7
AuthorsWalker GC
TitleTo cleave or not to cleave? Insights from the LexA crystal structure.
[30]
CommentsModel
PubMed ID14769061
JournalJ Biomol Struct Dyn
Year2004
Volume21
Pages681-9
AuthorsChattopadhyaya R, Pal A
TitleImproved model of a LexA repressor dimer bound to recA operator.
Related PDB1mvd
[31]
PubMed ID15929009
JournalJ Biomol NMR
Year2005
Volume31
Pages371-2
AuthorsOkon M, Pfuetzner RA, Vuckovic M, Little JW, Strynadka NC, McIntosh LP
TitleBackbone chemical shift assignments of the LexA catalytic domain in its active conformation.

comments
This enzyme belongs to the peptidase family-S24.
This enzyme performs auto-catalysis (or auto-hydrolysis).
According to the literature [4], [10], [13] & [28], this enzyme catalyzes the following reaction:
(1) Lys156 acts as a general base to deprotonate the nucleophile, Ser119.
(2) Ser119 makes a nucleophilic attack on the carbonyl carbon atom of the target peptide bond (Ala84-Gly85), leading to a tetrahedral transition state.
(3) The negative charge of the tetrahedral transition state is stabilized by the oxyanion hole, composed of mainchain amide groups of Met118/Ser119.
(4) Lys156 acts as a general acid to protonate the leaving amino group, forming an intermediate.
(5) Lys156 probably acts as a general base to deprotonate and activate a water molecule.
(6) The activated water makes a nucleophilic attack on the carbonyl carbon of the intermediate.
(7) Lys156 acts as a general acid to protonate Ser119, completing the reaction.

createdupdated
2003-08-222011-02-21


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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