EzCatDB: S00512

DB codeS00512
RLCP classification1.13.30000.16
CATH domainDomain 13.40.710.10Catalytic domain
E.C.3.5.2.6
CSA2blt

CATH domainRelated DB codes (homologues)
3.40.710.10S00513,S00529,S00414,T00222

Enzyme Name
Swiss-protKEGG

P05364P00811Q46041
Protein nameBeta-lactamaseBeta-lactamase
beta-lactamase
penicillinase
cephalosporinase
neutrapen
penicillin beta-lactamase
exopenicillinase
ampicillinase
penicillin amido-beta-lactamhydrolase
penicillinase I, II
beta-lactamase I-III
beta-lactamase A, B, C
beta-lactamase AME I
cephalosporin-beta-lactamase
SynonymsEC 3.5.2.6
Cephalosporinase
EC 3.5.2.6
Cephalosporinase
Beta-lactamase

KEGG pathways
MAP codePathways
MAP00311Penicillin and cephalosporin biosynthesis
MAP00312beta-Lactam resistance

Swiss-prot:Accession NumberP05364P00811Q46041
Entry nameAMPC_ENTCLAMPC_ECOLIQ46041_CITFR
ActivityA beta-lactam + H(2)O = a substituted beta- amino acid.A beta-lactam + H(2)O = a substituted beta- amino acid.
Subunit
Monomer.
Subcellular locationPeriplasm (By similarity).Periplasm.
Cofactor




SubstratesProductsintermediates
KEGG-idC01866C00395C00875C00001C03806
Compoundbeta-LactamPenicillinCephalosporinH2OSubstituted beta-amino acid
Typeamide groupamide group,carboxyl group,sulfide groupamide group,amine group,carboxyl group,sulfide groupH2Oamino acids
1blsAUnboundUnboundUnbound
UnboundTransition-state-analogue:IPP
1blsBUnboundUnboundUnbound
UnboundTransition-state-analogue:IPP
1gceAUnboundUnboundUnbound
UnboundUnbound
1c3bAUnboundUnboundUnbound
UnboundTransition-state-analogue:BZB
1c3bBUnboundUnboundUnbound
UnboundTransition-state-analogue:BZB
1fcmAUnboundUnboundUnbound
UnboundIntermediate-analogue:CXN
1fcmBUnboundUnboundUnbound
UnboundIntermediate-analogue:CXN
1fcnAUnboundUnboundUnbound
UnboundIntermediate-analogue:LOR
1fcnBUnboundUnboundUnbound
UnboundIntermediate-analogue:LOR
1fcoAUnboundUnboundUnbound
UnboundIntermediate-analogue:MOX
1fcoBUnboundUnboundUnbound
UnboundIntermediate-analogue:MOX
1fswAUnboundUnboundUnbound
UnboundTransition-state-analogue:CTB
1fswBUnboundUnboundUnbound
UnboundTransition-state-analogue:CTB
1fsyAUnboundUnboundUnbound
UnboundTransition-state-analogue:105
1fsyBUnboundUnboundUnbound
UnboundTransition-state-analogue:105
2blsAUnboundUnboundUnbound
UnboundUnbound
2blsBUnboundUnboundUnbound
UnboundUnbound
2bltAUnboundUnboundUnbound
UnboundUnbound
2bltBUnboundUnboundUnbound
UnboundUnbound
3blsAUnboundUnboundUnbound
UnboundTransition-state-analogue:APB
3blsBUnboundUnboundUnbound
UnboundTransition-state-analogue:APB
1fr1AUnboundUnboundUnbound
UnboundUnbound
1fr1BUnboundUnboundUnbound
UnboundUnbound
1fr6AUnboundUnboundUnbound
UnboundIntermediate-analogue:AZR
1fr6BUnboundUnboundUnbound
UnboundIntermediate-analogue:AZR

Active-site residues
pdbCatalytic residuesMain-chain involved in catalysiscomment
1blsASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

1blsBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

1gceASER 64;LYS 67;TYR 150;LYS 318;THR 319
SER 64;SER 321

1c3bASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

1c3bBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

1fcmASER 61;LYS 64;       ;LYS 312;THR 313
SER 61;ALA 315
mutant Q117L, Y147E
1fcmBSER 61;LYS 64;       ;LYS 312;THR 313
SER 61;ALA 315
mutant Q117L, Y147E
1fcnASER 61;LYS 64;       ;LYS 312;THR 313
SER 61;ALA 315
mutant Q117L, Y147E
1fcnBSER 61;LYS 64;       ;LYS 312;THR 313
SER 61;ALA 315
mutant Q117L, Y147E
1fcoASER 61;LYS 64;TYR 147;LYS 312;THR 313
SER 61;ALA 315

1fcoBSER 61;LYS 64;TYR 147;LYS 312;THR 313
SER 61;ALA 315

1fswASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

1fswBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

1fsyASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

1fsyBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

2blsASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

2blsBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

2bltASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

2bltBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

3blsASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

3blsBSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;ALA 318

1fr1ASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

1fr1BSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

1fr6ASER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318

1fr6BSER 64;LYS 67;TYR 150;LYS 315;THR 316
SER 64;SER 318


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.33
[2]p.11261
[4]p.6767-6771
[5]Fig.7, p.8584-85862
[11]p.2334-2336
[12]Fig.1, p.10511-10512
[14]Fig.22
[15]p.4619-4620
[17]p.6238-6239
[22]Fig.1(A), Fig.5, p.418-419, p.4212
[26]p.180
[29]p.1768-1769

references
[1]
CommentsX-ray crystallography (2.0 Angstroms)
PubMed ID2300174
JournalNature
Year1990
Volume343
Pages284-8
AuthorsOefner C, D'Arcy A, Daly JJ, Gubernator K, Charnas RL, Heinze I, Hubschwerlen C, Winkler FK
TitleRefined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis.
Related PDB1fr1,1fr6
[2]
CommentsX-ray crystallography (2 Angstroms)
Medline ID94068583
PubMed ID8248237
JournalProc Natl Acad Sci U S A
Year1993
Volume90
Pages11257-61
AuthorsLobkovsky E, Moews PC, Liu H, Zhao H, Frere JM, Knox JR
TitleEvolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase.
Related PDB2blt
Related Swiss-protP05364
[3]
PubMed ID8172894
JournalBiochemistry
Year1994
Volume33
Pages5193-201
AuthorsMonnaie D, Dubus A, Cooke D, Marchand-Brynaert J, Normark S, Frere JM
TitleRole of residue Lys315 in the mechanism of action of the Enterobacter cloacae 908R beta-lactamase.
[4]
CommentsX-ray crystallography (2.3 Angstroms)
Medline ID94263990
PubMed ID8204611
JournalBiochemistry
Year1994
Volume33
Pages6762-72
AuthorsLobkovsky E, Billings EM, Moews PC, Rahil J, Pratt RF, Knox JR
TitleCrystallographic structure of a phosphonate derivative of the Enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition-state analog.
Related PDB1bls
Related Swiss-protP05364
[5]
PubMed ID8031792
JournalBiochemistry
Year1994
Volume33
Pages8577-86
AuthorsDubus A, Normark S, Kania M, Page MG
TitleThe role of tyrosine 150 in catalysis of beta-lactam hydrolysis by AmpC beta-lactamase from Escherichia coli investigated by site-directed mutagenesis.
[6]
CommentsX-ray crystallography (2.0-2.3 Angstroms)
Medline ID99036630
PubMed ID9819201
JournalBiochemistry
Year1998
Volume37
Pages16082-92
AuthorsUsher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ
TitleThree-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design.
Related PDB2bls
Related Swiss-protP00811
[7]
PubMed ID9931012
JournalBiochemistry
Year1999
Volume38
Pages1469-77
AuthorsAdediran SA, Pratt RF
TitleBeta-secondary and solvent deuterium kinetic isotope effects on catalysis by the Streptomyces R61 DD-peptidase: comparisons with a structurally similar class C beta-lactamase.
[8]
PubMed ID10049265
JournalAntimicrob Agents Chemother
Year1999
Volume43
Pages543-8
AuthorsTrepanier S, Knox JR, Clairoux N, Sanschagrin F, Levesque RC, Huletsky A
TitleStructure-function studies of Ser-289 in the class C beta-lactamase from Enterobacter cloacae P99.
[9]
PubMed ID10393100
JournalBiochem J
Year1999
Volume341
Pages409-13
AuthorsRhazi N, Galleni M, Page MI, Frere JM
TitlePeptidase activity of beta-lactamases.
[10]
CommentsX-ray crystallography (1.8 Angstroms)
PubMed ID10441119
JournalBiochemistry
Year1999
Volume38
Pages10256-61
AuthorsCrichlow GV, Kuzin AP, Nukaga M, Mayama K, Sawai T, Knox JR
TitleStructure of the extended-spectrum class C beta-lactamase of Enterobacter cloacae GC1, a natural mutant with a tandem tripeptide insertion.
Related PDB1gce
[11]
CommentsX-ray crystallography (2.25 Angstroms)
Medline ID20060984
PubMed ID10595535
JournalProtein Sci
Year1999
Volume8
Pages2330-2337
AuthorsPowers RA, Blazquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK
TitleThe complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
Related PDB1c3b
Related Swiss-protP00811
[12]
JournalJ Am Chem Soc
Year2000
Volume122
Pages10504-12
AuthorsPatera A, Blaszczak LC, Shoichet BK
TitleCrystal structures of substrate and inhibitor complexes with ampc -lactamase: possible implications for substrate-assisted catalysis.
Related PDB1fcm,1fcn,1fco
[13]
PubMed ID11134945
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages162-4
AuthorsWouters J, Charlier P, Monnaie D, Frere JM, Fonze E
TitleExpression, purification, crystallization and preliminary X-ray analysis of the native class C beta-lactamase from Enterobacter cloacae 908R and two mutants.
[14]
CommentsX-ray crystallography (1.75/1.90 Angstroms)
PubMed ID11182316
JournalChem Biol
Year2001
Volume8
Pages17-31
AuthorsCaselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK
TitleEnergetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.
Related PDB1fsw,1fsy
[15]
PubMed ID11294628
JournalBiochemistry
Year2001
Volume40
Pages4610-21
AuthorsKaur K, Pratt RF
TitleMechanism of reaction of acyl phosph(on)ates with the beta-lactamase of Enterobacter cloacae P99.
[16]
PubMed ID11300697
JournalBioorg Chem
Year2001
Volume29
Pages77-95
AuthorsSlater MJ, Laws AP, Page MI
TitleThe relative catalytic efficiency of beta-lactamase catalyzed acyl and phosphyl transfer.
[17]
PubMed ID11371184
JournalBiochemistry
Year2001
Volume40
Pages6233-9
AuthorsCrichlow GV, Nukaga M, Doppalapudi VR, Buynak JD, Knox JR
TitleInhibition of class C beta-lactamases: structure of a reaction intermediate with a cephem sulfone.
[18]
PubMed ID11434768
JournalBiochemistry
Year2001
Volume40
Pages7992-9
AuthorsTrehan I, Beadle BM, Shoichet BK
TitleInhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.
[19]
PubMed ID11478888
JournalBiochemistry
Year2001
Volume40
Pages9207-14
AuthorsPowers RA, Caselli E, Focia PJ, Prati F, Shoichet BK
TitleStructures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design.
[20]
PubMed ID11709298
JournalAntimicrob Agents Chemother
Year2001
Volume45
Pages3279-86
AuthorsRudgers GW, Huang W, Palzkill T
TitleBinding properties of a peptide derived from beta-lactamase inhibitory protein.
[21]
PubMed ID11914079
JournalBiochemistry
Year2002
Volume41
Pages4329-38
AuthorsBell JH, Pratt RF
TitleMechanism of inhibition of the beta-lactamase of Enterobacter cloacae P99 by 1:1 complexes of vanadate with hydroxamic acids.
[22]
PubMed ID12005439
JournalStructure (Camb)
Year2002
Volume10
Pages413-24
AuthorsBeadle BM, Trehan I, Focia PJ, Shoichet BK
TitleStructural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
[23]
PubMed ID12121656
JournalStructure (Camb)
Year2002
Volume10
Pages1013-23
AuthorsPowers RA, Morandi F, Shoichet BK
TitleStructure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.
[24]
PubMed ID12435704
JournalAntimicrob Agents Chemother
Year2002
Volume46
Pages3978-80
AuthorsBeadle BM, Shoichet BK
TitleStructural basis for imipenem inhibition of class C beta-lactamases.
[25]
PubMed ID12482929
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages16537-42
AuthorsBaker K, Bleczinski C, Lin H, Salazar-Jimenez G, Sengupta D, Krane S, Cornish VW
TitleChemical complementation: a reaction-independent genetic assay for enzyme catalysis.
[26]
PubMed ID12513696
JournalBiochem J
Year2003
Volume371
Pages175-81
AuthorsKato-Toma Y, Iwashita T, Masuda K, Oyama Y, Ishiguro M
TitlepKa measurements from nuclear magnetic resonance of tyrosine-150 in class C beta-lactamase.
[27]
PubMed ID12696055
JournalProteins
Year2003
Volume51
Pages442-52
AuthorsFenollar-Ferrer C, Frau J, Donoso J, Munoz F
TitleRole of beta-lactam carboxyl group on binding of penicillins and cephalosporins to class C beta-lactamases.
[28]
PubMed ID12904027
JournalJ Am Chem Soc
Year2003
Volume125
Pages9612-8
AuthorsMeroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S
TitleStructural aspects for evolution of beta-lactamases from penicillin-binding proteins.
[29]
PubMed ID14521155
JournalCell Mol Life Sci
Year2003
Volume60
Pages1764-73
AuthorsWouters J, Fonze E, Vermeire M, Frere JM, Charlier P
TitleCrystal structure of Enterobacter cloacae 908R class C beta-lactamase bound to iodo-acetamido-phenyl boronic acid, a transition-state analogue.

comments
This enzyme belongs to the class-C beta-lactamase family.
Ser64 acts as a nucleophile, making a nucleophilic attack on beta-lactam ring, to form acyl-enzyme intermediate.
According to the early studies ([1], [3], [4] & [5]), Tyr150 was considered to function as general acid-base.
In contrast, the more recent report, [22], suggested substrate-assisted base. In this reported mechanism, C4' carboxylate of the substrate may activate Tyr150, which in turn may activate Ser64 by abstracting a proton from the serine residue during the acylation step [22]. Lys67 might play an intermediary role in transfer of the proton [22].
In the next deacylation step, a water molecule bound to Thr316 (and possibly Tyr150) makes an attack on the C8 carbonyl carbon of the acyl-enzyme intermediate, activating the Ser64 to be a leaving group [22].
The role of Tyr150 seems to be still controversial. However, considering the structure with ligand, Ser64, Tyr150, and Lys150 act as a nucleophile, acid-base, and a modulator for acid-base. Here, mainchain amide groups of Ser64 and Ser318 form an oxyanion hole. These suggest that the mechanism is very similar to that of trypsin (D00197).

createdupdated
2002-09-272009-10-01
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 2010)
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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.