DB code: S00502

RLCP classification 1.13.11100.285 : Hydrolysis
CATH domain 3.40.80.10 : Lysozyme-like Catalytic domain
E.C. 3.5.1.28
CSA 1lba
M-CSA 1lba
MACiE

CATH domain Related DB codes (homologues)
3.40.80.10 : Lysozyme-like S00535 S00536

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00806 N-acetylmuramoyl-L-alanine amidase
EC 3.5.1.28
T7 lysozyme
NP_041973.1 (Protein)
NC_001604.1 (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
P00806 NAAA_BPT7 Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. Zinc, required for amidase activity.

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
1aroL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound
1lbaA 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 [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1aroL Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 1046;LYS 1128 HIS 1017;HIS 1122;CYS 1130(Zinc binding)
1lbaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 46;LYS 128 HIS 17;HIS 122;CYS 130(Zinc binding) mutant deletion 2-5, mutant A6K

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
According to the literature [2] and [10], the reaction proceeds as follows:
(1) Tyr46 acts as a general base to activate the hydrolytic water, along with the Zinc ion bound to His17/His122/Cys130. 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 Lys128.
(4) Tyr46 acts as a general acid to protonate the leaving amine group, completing the hydrolysis.

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