DB code: S00536

RLCP classification 1.13.11100.286 : Hydrolysis
CATH domain 3.40.80.10 : Lysozyme-like Catalytic domain
E.C. 3.5.1.28
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.80.10 : Lysozyme-like S00502 S00535

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q8INK6 Peptidoglycan-recognition protein-LB
EC 3.5.1.28
NP_001247053.1 (Protein)
NM_001260124.1 (DNA/RNA sequence)
NP_001247054.1 (Protein)
NM_001260125.1 (DNA/RNA sequence)
NP_650079.1 (Protein)
NM_141822.3 (DNA/RNA sequence)
NP_731575.1 (Protein)
NM_169392.2 (DNA/RNA sequence)
NP_731576.1 (Protein)
NM_169393.2 (DNA/RNA sequence)
PF01510 (Amidase_2)
[Graphical View]

KEGG enzyme name
N-acetylmuramoyl-L-alanine amidase
acetylmuramyl-L-alanine amidase
N-acetylmuramyl-L-alanine amidase
N-acylmuramyl-L-alanine amidase
acetylmuramoyl-alanine amidase
N-acetylmuramic acid L-alanine amidase
acetylmuramyl-alanine amidase
N-acetylmuramylalanine amidase
murein hydrolase
N-acetylmuramoyl-L-alanine amidase type I
N-acetylmuramoyl-L-alanine amidase type II

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q8INK6 PGPLB_DROME Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. Monomer. Isoform C: Secreted (Potential). Binds 1 zinc ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00550 Peptidoglycan biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 L00022 C00001 C05887 C00012
E.C.
Compound Zinc Glycopeptide containing N-acetylmuramoyl-peptide H2O N-Acetyl-D-muramoate Peptide
Type heavy metal amide group,peptide/protein,polysaccharide H2O amide group,carbohydrate,carboxyl group peptide/protein
ChEBI 29105
15377
PubChem 32051
22247451
962
1ohtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ohtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 78;HIS 43 HIS 42;HIS 152;CYS 160(Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.4037
[8]
p.836-838
[9]
p.789-791
[10]
Scheme 1, p.118-119 3
[11]
p.35435-35439

References
[1]
Resource
Comments
Medline ID
PubMed ID 4582731
Journal J Biol Chem
Year 1973
Volume 248
Pages 7247-52
Authors Inouye M, Arnheim N, Sternglanz R
Title Bacteriophage T7 lysozyme is an N-acetylmuramyl-L-alanine amidase.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND REVISION TO 118.
Medline ID 94224877
PubMed ID 8171031
Journal Proc Natl Acad Sci U S A
Year 1994
Volume 91
Pages 4034-8
Authors Cheng X, Zhang X, Pflugrath JW, Studier FW
Title The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase.
Related PDB 1lba
Related UniProtKB P00806
[3]
Resource
Comments
Medline ID
PubMed ID 9405156
Journal J Mol Biol
Year 1997
Volume 274
Pages 748-56
Authors Jeruzalmi D, Steitz TA
Title Use of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF COMPLEX WITH POLYMERASE.
Medline ID 98336199
PubMed ID 9670025
Journal EMBO J
Year 1998
Volume 17
Pages 4101-13
Authors Jeruzalmi D, Steitz TA
Title Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
Related PDB 1aro
Related UniProtKB P00806
[5]
Resource
Comments
Medline ID
PubMed ID 9719635
Journal J Mol Biol
Year 1998
Volume 281
Pages 793-802
Authors Villemain J, Sousa R
Title Specificity in transcriptional regulation in the absence of specific DNA binding sites: the case of T7 lysozyme.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10543943
Journal J Mol Biol
Year 1999
Volume 293
Pages 457-75
Authors Huang J, Villemain J, Padilla R, Sousa R
Title Mechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase during different phases of transcription.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10679468
Journal Curr Opin Struct Biol
Year 2000
Volume 10
Pages 117-23
Authors Cheetham GM, Steitz TA
Title Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 12654266
Journal J Mol Biol
Year 2003
Volume 327
Pages 833-42
Authors Liepinsh E, Genereux C, Dehareng D, Joris B, Otting G
Title NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.
Related PDB 1iya 1j2s
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12845326
Journal Nat Immunol
Year 2003
Volume 4
Pages 787-93
Authors Kim MS, Byun M, Oh BH
Title Crystal structure of peptidoglycan recognition protein LB from Drosophila melanogaster.
Related PDB 1oht
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 14507260
Journal Biochem J
Year 2004
Volume 377
Pages 111-20
Authors Genereux C, Dehareng D, Devreese B, Van Beeumen J, Frere JM, Joris B
Title Mutational analysis of the catalytic centre of the Citrobacter freundii AmpD N-acetylmuramyl-L-alanine amidase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 16103125
Journal J Biol Chem
Year 2005
Volume 280
Pages 35433-9
Authors Low LY, Yang C, Perego M, Osterman A, Liddington RC
Title Structure and lytic activity of a Bacillus anthracis prophage endolysin.
Related PDB
Related UniProtKB

Comments
This enzyme is homologous to bacteriophage T7 lysozyme (S00502 in EzCatDB). However, the catalytic residues are not completely the same as those by its homologue. Instead of Lys128 in T7 lysozyme, either His43 or His67 may acts as a stabilizer, according to the literature [9]. Considering its active site, His43 must acts as a stabilizer, which stabilize the negative charge on the transition-state.
According to the literature [2], [9] and [10], the reaction proceeds as follows:
(1) Tyr78 acts as a general base to activate the hydrolytic water, along with the Zinc ion bound to His42/His152/Cys160. Here, the zinc ion polarizes the carbonyl group of the scissile bond.
(2) The activated water makes a nucleophilic attack on the target carbonyl carbon.
(3) The transition-state is stabilized by both Zinc ion and His43.
(4) Tyr78 acts as a general acid to protonate the leaving amine group, completing the hydrolysis.

Created Updated
2004-05-11 2009-02-26