DB code: S00437

RLCP classification 1.13.30185.55 : Hydrolysis
CATH domain 3.60.60.10 : Penicillin V Acylase; Chain A Catalytic domain
E.C. 3.5.1.11
CSA
M-CSA
MACiE M0241

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
P12256 Penicillin acylase
EC 3.5.1.11
Penicillin V amidase
PVA
C59.001 (Cysteine)
PF02275 (CBAH)
[Graphical View]

KEGG enzyme name
penicillin amidase
penicillin acylase
benzylpenicillin acylase
novozym 217
semacylase
alpha-acylamino-beta-lactam acylhydrolase
ampicillin acylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P12256 PAC_BACSH Penicillin + H(2)O = a carboxylate + 6- aminopenicillanate. Homotetramer.

KEGG Pathways
Map code Pathways E.C.
MAP00311 Penicillin and cephalosporin biosynthesis

Compound table
Substrates Products Intermediates
KEGG-id C00395 C00001 C00060 C02954
E.C.
Compound Penicillin H2O Carboxylate 6-Aminopenicillanate
Type carboxyl group,peptide/protein,sulfide group H2O carboxyl group amide group,amine group,carboxyl group,sulfide group
ChEBI 15377
16705
57869
PubChem 22247451
962
11082
7057887
2pvaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pvaB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pvaC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pvaD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pvaH Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1] & [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2pvaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 20;ASN 175;ARG 228 OCS 1 TYR 82 OCS,Cysteinesulfonic acid
2pvaB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 20;ASN 175;ARG 228 OCS 1 TYR 82 OCS,Cysteinesulfonic acid
2pvaC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 20;ASN 175;ARG 228 OCS 1 TYR 82 OCS,Cysteinesulfonic acid
2pvaD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 20;ASN 175;ARG 228 OCS 1 TYR 82 OCS,Cysteinesulfonic acid
3pvaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaG Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82
3pvaH Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1;ASP 20;ASN 175;ARG 228 TYR 82

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.3 5
[3]
p.239
[4]
p.414
[6]
Fig.2 3
[7]
p.146-147

References
[1]
Resource
Comments Penicillin G acylase (homologous enzyme)
Medline ID
PubMed ID 7816145
Journal Nature
Year 1995
Volume 373
Pages 264-8
Authors Duggleby HJ, Tolley SP, Hill CP, Dodson EJ, Dodson G, Moody PC
Title Penicillin acylase has a single-amino-acid catalytic centre.
Related PDB
Related UniProtKB
[2]
Resource
Comments Penicillin G acylase (homologous enzyme)
Medline ID
PubMed ID 7477383
Journal Nature
Year 1995
Volume 378
Pages 416-9
Authors Brannigan JA, Dodson G, Duggleby HJ, Moody PC, Smith JL, Tomchick DR, Murzin AG
Title A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.
Related PDB
Related UniProtKB
[3]
Resource
Comments Penicillin G acylase (homologous enzyme)
Medline ID
PubMed ID 9931321
Journal Biochem J
Year 1999
Volume 338
Pages 235-9
Authors Morillas M, Goble ML, Virden R
Title The kinetics of acylation and deacylation of penicillin acylase from Escherichia coli ATCC 11105: evidence for lowered pKa values of groups near the catalytic centre.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10331865
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 414-416
Authors Suresh CG, Pundle AV, SivaRaman H, Rao KN, Brannigan JA, McVey CE, Verma CS, Dauter Z, Dodson EJ, Dodson GG
Title Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members.
Related PDB 2pva 3pva
Related UniProtKB
[5]
Resource
Comments Penicillin G acylase (homologous enzyme)
Medline ID
PubMed ID 10993730
Journal J Mol Biol
Year 2000
Volume 302
Pages 887-98
Authors Hewitt L, Kasche V, Lummer K, Lewis RJ, Murshudov GN, Verma CS, Dodson GG, Wilson KS
Title Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography, catalysis; Penicillin G acylase (homologous enzyme)
Medline ID
PubMed ID 11239085
Journal Protein Eng
Year 2000
Volume 13
Pages 857-863
Authors Alkema WB, Hensgens CM, Kroezinga EH, de Vries E, Floris R, van der Laan JM, Dijkstra BW, Janssen DB
Title Characterization of the beta-lactam binding site of penicillin acylase of Escherichia coli by structural and site-directed mutagenesis studies.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-ray crystallography (1.3 Angstroms), catalysis; Penicillin G acylase (homologous enzyme)
Medline ID
PubMed ID 11601852
Journal J Mol Biol
Year 2001
Volume 313
Pages 139-150
Authors McVey CE, Walsh MA, Dodson GG, Wilson KS, Brannigan JA
Title Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to N-terminal nucleophile (Ntn) hydrolase family, of which sidechain of the N-terminal residue acts as nucleophile, assisted by its own alpha-amino group.
The paper [1] proposed the catalytic mechanism of the homologous enzyme, penicillin G acylase, whose nucleophilic residue is serine instead of cysteine.
(1) The alpha-amino group enhances the nucleophilicity of the sidechain of the N-terminal residue, through the bridging water between them.
(2) The sidechain of Cys1 makes a nucleophilic attack on the acyl carbon of penicillin, forming an oxyanion tetrahedral, stabilized by the oxyanion hole composed of mainchain amides and sidechain of Asn175. Here, the alpha-amino group protonates the leaving amine group through a water.
(3) This tetrahedral intermediate will then collapse to form an acyl enzyme and release the free 6-aminopenicillanic acid.
(4) The acyl enzyme will be attacked by water to form a second tetrahedral intermediate, stabilized by the same oxyanion hole, which can in turn collapse to release the free phenylacetic acid.
In contrast, the literature [7] suggested that the catalytic mechanism proceeds via direct nucleophilic attack of the nucleophilic residue on the scissile amide and not as via the bridging water molecule acting as a "virtual" base.
According to the paper [3], the residue corresponding to Arg228 in its homologue, penicillin G acylase, seems to be important for catalysis, orienting the N-terminal catalytic residue and contributing to a decrease in the pKa of alpha-amino group.
The literature on this enzyme [4] reported that the oxyanion hole consists of the sidechain of Asn175 and NH of Tyr82, whilst Arg228, Asp20 and Asn175 are critical for positioning the lone pair of the unprotonated N-terminal alpha-amino group. This might lead to the decrease in the pKa of the alpha-amino group.

Created Updated
2002-09-04 2009-02-26