EzCatDB: S00414
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DB codeS00414
RLCP classification1.13.30015.15 : Hydrolysis
CATH domainDomain 13.40.710.10 : Beta-lactamaseCatalytic domain
E.C.3.4.16.4

CATH domainRelated DB codes (homologues)
3.40.710.10 : Beta-lactamaseS00512,S00513,S00529,T00222

Enzyme Name
UniProtKBKEGG

P15555
Protein nameD-alanyl-D-alanine carboxypeptidaseserine-type D-Ala-D-Ala carboxypeptidase
DD-peptidase
D-alanyl-D-alanine-carboxypeptidase
D-alanyl-D-alanine-cleaving-peptidase
D-alanyl-D-alanine-cleaving peptidase
DD-transpeptidase
D-alanine carboxypeptidase
DD-carboxypeptidase
D-alanyl carboxypeptidase
SynonymsDD-carboxypeptidase
DD-peptidase
EC 3.4.16.4
MEROPSS12.001 (Serine)
PfamPF00144 (Beta-lactamase)
[Graphical view]


UniProtKB:Accession NumberP15555
Entry nameDAC_STRSR
ActivityPreferential cleavage: (Ac)(2)-L-Lys-D-Ala-|- D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Subunit
Subcellular locationSecreted.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00012C00001C03326C00133C00012C02487I00087I00085I00086
CompoundPeptideH2O(Ac)2-L-Lys-D-Ala-D-AlaD-AlaninePeptide(Ac)2-L-Lys-D-AlaPeptidyl-tetrahedral intermediateAcyl-enzymeTetrahedral intermediate
Typepeptide/proteinH2Oamino acids,amide group,carboxyl group,lipid,peptide/proteinamino acidspeptide/proteinamino acids,amide group,carboxyl group,peptide/protein,lipid,peptide/protein


ChEBI
15377
270
15570
57416

269



PubChem
962
22247451
152678
7311725
71080

5462243



                 
1cefAUnbound UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1cegAUnbound UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1hvbAUnbound UnboundUnboundUnboundUnboundUnboundIntermediate-analogue:CEHUnbound
3pteAUnbound UnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residuesMain-chain involved in catalysis
          
1cefASER 62;LYS 65;TYR 159;ASN 161
SER 62;THR 301
1cegASER 62;LYS 65;TYR 159;ASN 161
SER 62;THR 301
1hvbASER 62;LYS 65;TYR 159;ASN 161
SER 62;THR 301
3pteASER 62;LYS 65;TYR 159;ASN 161
SER 62;THR 301

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.499
[4]p.100-101
[5]Scheme I, Scheme III
[6]p.482-483
[7]p.491-493
[8]p.359-361
[9]p.9534-9540
[10]p.227-233
[11]p.380
[12]p.731
[13]Scheme 3, p.1476
[15]p.976
[16]p.1429
[19]p.472-476
[20]Fig.6, p.1202-1207

references
[1]
CommentsX-ray crystallography (2.8 Angstroms)
Medline ID85207640
PubMed ID3997832
JournalJ Biol Chem
Year1985
Volume260
Pages6449-58
AuthorsKelly JA, Knox JR, Moews PC, Hite GJ, Bartolone JB, Zhao H, Joris B, Frere JM, Ghuysen JM
Title2.8-A Structure of penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase from Streptomyces R61 and complexes with beta-lactams.
Related UniProtKBP15555
[2]
CommentsX-ray crystallography
Medline ID90351121
PubMed ID2386365
JournalAntimicrob Agents Chemother
Year1990
Volume34
Pages1342-7
AuthorsKnox JR, Pratt RF
TitleDifferent modes of vancomycin and D-alanyl-D-alanine peptidase binding to cell wall peptide and a possible role for the vancomycin resistance protein.
Related UniProtKBP15555
[3]
PubMed ID1546964
JournalBiochem J
Year1992
Volume282
Pages495-500
AuthorsHadonou AM, Jamin M, Adam M, Joris B, Dusart J, Ghuysen JM, Frere JM
TitleImportance of the His-298 residue in the catalytic mechanism of the Streptomyces R61 extracellular DD-peptidase.
[4]
PubMed ID1628665
JournalEur J Biochem
Year1992
Volume207
Pages97-102
AuthorsHadonou AM, Wilkin JM, Varetto L, Joris B, Lamotte-Brasseur J, Klein D, Duez C, Ghuysen JM, Frere JM
TitleSite-directed mutagenesis of the Streptomyces R61 DD-peptidase. Catalytic function of the conserved residues around the active site and a comparison with class-A and class-C beta-lactamases.
[5]
PubMed ID8343517
JournalBiochemistry
Year1993
Volume32
Pages7278-85
AuthorsJamin M, Wilkin JM, Frere JM
TitleA new kinetic mechanism for the concomitant hydrolysis and transfer reactions catalyzed by bacterial DD-peptidases.
[6]
PubMed ID8042992
JournalBiochem J
Year1994
Volume301
Pages477-83
AuthorsWilkin JM, Dubus A, Joris B, Frere JM
TitleThe mechanism of action of DD-peptidases: the role of Threonine-299 and -301 in the Streptomyces R61 DD-peptidase.
[7]
PubMed ID8042993
JournalBiochem J
Year1994
Volume301
Pages485-94
AuthorsDubus A, Wilkin JM, Raquet X, Normark S, Frere JM
TitleCatalytic mechanism of active-site serine beta-lactamases: role of the conserved hydroxy group of the Lys-Thr(Ser)-Gly triad.
[8]
PubMed ID7980393
JournalBiochem J
Year1994
Volume303
Pages357-62
Authorsvan der Linden MP, de Haan L, Dideberg O, Keck W
TitleSite-directed mutagenesis of proposed active-site residues of penicillin-binding protein 5 from Escherichia coli.
[9]
CommentsX-ray crystallography (1.8/2.0 Angstroms)
PubMed ID7626623
JournalBiochemistry
Year1995
Volume34
Pages9532-40
AuthorsKuzin AP, Liu H, Kelly JA, Knox JR
TitleBinding of cephalothin and cefotaxime to D-ala-D-ala-peptidase reveals a functional basis of a natural mutation in a low-affinity penicillin-binding protein and in extended-spectrum beta-lactamases.
Related PDB1cef,1ceg
[10]
CommentsX-ray crystallography (1.6 Angstroms)
Medline ID96083824
PubMed ID7490745
JournalJ Mol Biol
Year1995
Volume254
Pages223-36
AuthorsKelly JA, Kuzin AP
TitleThe refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution.
Related PDB3pte
Related UniProtKBP15555
[11]
PubMed ID9359404
JournalBiochem J
Year1997
Volume327
Pages377-81
AuthorsZhao GH, Duez C, Lepage S, Forceille C, Rhazi N, Klein D, Ghuysen JM, Frere JM
TitleSite-directed mutagenesis of the Actinomadura R39 DD-peptidase.
[12]
PubMed ID9711239
JournalCell Mol Life Sci
Year1998
Volume54
Pages726-32
AuthorsWilkin JM, Lamotte-Brasseur J, Frere JM
TitleThe catalytic mechanism of DD-peptidases: unexpected importance of tyrosine 280 in the transpeptidation reaction catalysed by the Streptomyces R61 DD-peptidase.
[13]
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.
[14]
PubMed ID10393100
JournalBiochem J
Year1999
Volume341
Pages409-13
AuthorsRhazi N, Galleni M, Page MI, Frere JM
TitlePeptidase activity of beta-lactamases.
[15]
PubMed ID10986464
JournalStructure Fold Des
Year2000
Volume8
Pages971-80
AuthorsBompard-Gilles C, Remaut H, Villeret V, Prange T, Fanuel L, Delmarcelle M, Joris B, Frere J, Van Beeumen J
TitleCrystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
[16]
CommentsX-ray crystallography (1.2 Angstroms)
PubMed ID11171967
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages1427-31
AuthorsLee W, McDonough MA, Kotra L, Li ZH, Silvaggi NR, Takeda Y, Kelly JA, Mobashery S
TitleA 1.2-A snapshot of the final step of bacterial cell wall biosynthesis.
Related PDB1hvb
[17]
PubMed ID11325933
JournalJ Bacteriol
Year2001
Volume183
Pages3055-64
AuthorsNelson DE, Young KD
TitleContributions of PBP 5 and DD-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli.
[18]
PubMed ID11535797
JournalMicrobiology
Year2001
Volume147
Pages2571-8
AuthorsReynolds PE, Ambur OH, Casadewall B, Courvalin P
TitleThe VanY(D) DD-carboxypeptidase of Enterococcus faecium BM4339 is a penicillin-binding protein.
[19]
PubMed ID11847270
JournalProtein Sci
Year2002
Volume11
Pages467-78
AuthorsWagner UG, Petersen EI, Schwab H, Kratky C
TitleEstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity.
[20]
PubMed ID12564922
JournalBiochemistry
Year2003
Volume42
Pages1199-208
AuthorsSilvaggi NR, Anderson JW, Brinsmade SR, Pratt RF, Kelly JA
TitleThe crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state.
Related PDB1mpl
[21]
PubMed ID12646690
JournalProtein Eng
Year2003
Volume16
Pages27-35
AuthorsPeimbert M, Segovia L
TitleEvolutionary engineering of a beta-Lactamase activity on a D-Ala D-Ala transpeptidase fold.

comments
This enzyme belongs to peptidase family-S12. This enzyme can act as a bifunctional enzyme, catalyzing both hydrolysis and acyl group transfer reactions (see [5]).
The catalysis involves two steps, acylation and deacylation, as follows:
(1) During the first step for acylation, the catalytic Ser62 (PDB; 1cef) acts as a nucleophile, which makes an attack on the carbonyl carbon atom to form an acyl-enzyme, accoriding to the literature [9], [20].
(2) Despite no clear evidence, Tyr159 has been thought to act as a general base, which can activate the catalytic Ser62, according to the paper [9]. On the other hand, another paper [20] proposed that Tyr159 is the general acid for formation of the tetrahedral intermediate, by protonating the leaving group, whilst the neutral Lys65 can act as a general base in the acylation step.
(3) In the transition state, the tetrahedral geometry of the acyl group can be stablized by an oxyanion hole, made up by the main chain amides of Ser62 and Thr301.
(4) The second step involves the deacylation, which is the hydrolysis or transfer of the intermediate. According to the paper [20], the phenoxide anion of Tyr159 would act as a general base, by activating a deacylating water for a nucleophile attack on the acyl-enzyme. Here, a positive charge on Lys65 would function as a modulator, by stabilzing the phenoxide anion on Tyr159, and by polarizing the ester bond for the nucleophilic attack by the water molecule [20].
###
Moreover, Asn161 and His298 might act as modulator for Lys65 and Tyr159, respectively.
Taken together, Tyr159 acts as acid-base, whereas Lys65 acts as base-modulator.

createdupdated
2002-09-272011-02-16


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