DB code: S00529

CATH domain	3.40.710.10 : Beta-lactamase	Catalytic domain
E.C.	3.4.16.4
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.40.710.10 : Beta-lactamase	S00512 S00513 S00414 T00222

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	MEROPS	Pfam
P39042	D-alanyl-D-alanine carboxypeptidase	DD-carboxypeptidase DD-peptidase EC 3.4.16.4 Penicillin-binding protein PBP	S11.004 (Serine)	PF00768 (Peptidase_S11) [Graphical View]

KEGG enzyme name
serine-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

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P39042	DACX_STRSK	Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-\|- D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.		Secreted (Potential).

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates			Products			Intermediates
KEGG-id	C00012	C00001	C03326	C00133	C00012	C02487
E.C.
Compound	Peptide	H2O	(Ac)2-L-Lys-D-Ala-D-Ala	D-Alanine	Peptide	(Ac)2-L-Lys-D-Ala
Type	peptide/protein	H2O	amino acids,amide group,carboxyl group,lipid,peptide/protein	amino acids	peptide/protein	amino acids,amide group,carboxyl group,peptide/protein,lipid,peptide/protein
ChEBI		15377 15377	270 270	15570 57416 15570 57416		269 269
PubChem		22247451 962 22247451 962	152678 152678	71080 7311725 71080 7311725		5462243 5462243

1eqsA	Unbound		Unbound	Unbound	Unbound	Unbound
1es2A	Unbound		Unbound	Unbound	Unbound	Unbound
1es3A	Unbound		Unbound	Unbound	Unbound	Unbound
1es4A	Unbound		Unbound	Unbound	Unbound	Unbound
1es5A	Unbound		Unbound	Unbound	Unbound	Unbound
1esiA	Unbound		Unbound	Unbound	Unbound	Unbound
1j9mA	Unbound		Unbound	Unbound	Unbound	Unbound
1skfA	Unbound		Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1eqsA	SER 35; ;SER 96			SER 35;SER 216	mutant K38H
1es2A	SER 35;LYS 38;			SER 35;SER 216	mutant S96A
1es3A	SER 35;LYS 38;SER 96			SER 35;SER 216	mutant C98A
1es4A	SER 35;LYS 38;SER 96			SER 35;SER 216	mutant C98N
1es5A	SER 35;LYS 38;SER 96				mutant S216A
1esiA	SER 35;LYS 38;SER 96			SER 35;SER 216	mutant R248I
1j9mA	SER 35; ;SER 96			SER 35;SER 216	mutant K38H
1skfA	SER 35;LYS 38;SER 96			SER 35;SER 216

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	p.21856-21858

References
[1]
Resource
Comments	X-ray crystallography (2.0 Angstroms)
Medline ID
PubMed ID	10419503
Journal	J Biol Chem
Year	1999
Volume	274
Pages	21853-60
Authors	Fonze E, Vermeire M, Nguyen-Disteche M, Brasseur R, Charlier P
Title	The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of streptomyces K15.
Related PDB	1eqs 1es2 1es3 1es4 1es5 1esi 1skf
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	12627955
Journal	Biochemistry
Year	2003
Volume	42
Pages	2895-906
Authors	Rhazi N, Charlier P, Dehareng D, Engher D, Vermeire M, Frere JM, Nguyen-Disteche M, Fonze E
Title	Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.
Related PDB	1j9m
Related UniProtKB

Comments
Theis enzyme belongs either to peptidase family-S11. The enzyme can act as a bifunctional enzyme, catalyzing both hydrolysis and acyl group transfer reaction. The hydrolysis involves two steps, acylation and deacylation. The acylation proceeds as follows: (1) Despite no clear evidence, Lys38 has been implicated to act as a general base, which can activate the catalytic Ser35, according to the paper [2]. (2) The catalytic Ser35 acts as a nucleophile, which makes an attack on the carbonyl carbon atom to form an acyl-enzyme, accoriding to the literature [1], [2]. (3) An oxyanion hole, formed by mainchain amide groups of Ser35 and Ser216, stabilize the polarized carbonyl group of the substrate and tetrahedral intermediate during the transition state (see [2]). (4) Lys38 acts as a general acid to protonate the leaving nitrogen, through the hydroxyl group of Ser96. (Ser96 acts as a proton shuttle.) As for the deacylation, it has not been elucidated which residue can activate the hydrolytic water, which would attack the acyl-enzyme intermediate (see [2]). Probably, either Lys38 or Ser96 might play the role in activating the water (see [2]).

Comments

Theis enzyme belongs either to peptidase family-S11.
The enzyme can act as a bifunctional enzyme, catalyzing both hydrolysis and acyl group transfer reaction.
The hydrolysis involves two steps, acylation and deacylation. The acylation proceeds as follows:
(1) Despite no clear evidence, Lys38 has been implicated to act as a general base, which can activate the catalytic Ser35, according to the paper [2].
(2) The catalytic Ser35 acts as a nucleophile, which makes an attack on the carbonyl carbon atom to form an acyl-enzyme, accoriding to the literature [1], [2].
(3) An oxyanion hole, formed by mainchain amide groups of Ser35 and Ser216, stabilize the polarized carbonyl group of the substrate and tetrahedral intermediate during the transition state (see [2]).
(4) Lys38 acts as a general acid to protonate the leaving nitrogen, through the hydroxyl group of Ser96. (Ser96 acts as a proton shuttle.)
As for the deacylation, it has not been elucidated which residue can activate the hydrolytic water, which would attack the acyl-enzyme intermediate (see [2]). Probably, either Lys38 or Ser96 might play the role in activating the water (see [2]).

Created	Updated
2002-09-27	2009-02-26