EzCatDB: S00502
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00502
RLCP classification1.13.11100.285 : Hydrolysis
CATH domainDomain 13.40.80.10 : Lysozyme-likeCatalytic domain
E.C.3.5.1.28
CSA1lba

CATH domainRelated DB codes (homologues)
3.40.80.10 : Lysozyme-likeS00535,S00536

Enzyme Name
UniProtKBKEGG

P00806
Protein nameN-acetylmuramoyl-L-alanine amidaseN-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
SynonymsEC 3.5.1.28
T7 lysozyme
RefSeqNP_041973.1 (Protein)
NC_001604.1 (DNA/RNA sequence)
PfamPF01510 (Amidase_2)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00550Peptidoglycan biosynthesis

UniProtKB:Accession NumberP00806
Entry nameNAAA_BPT7
ActivityHydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
Subunit
Subcellular location
CofactorZinc, required for amidase activity.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038L00022C00001C05887C00012
CompoundZincGlycopeptide containing N-acetylmuramoyl-peptideH2ON-Acetyl-D-muramoatePeptide
Typeheavy metalamide group,peptide/protein,polysaccharideH2Oamide group,carbohydrate,carboxyl grouppeptide/protein
ChEBI29105

15377


PubChem32051

962
22247451


             
1aroLBound:_ZNUnbound UnboundUnbound
1lbaABound:_ZNUnbound UnboundUnbound

Active-site residues
resource
literature [2]
pdbCatalytic residuesCofactor-binding residuescomment
           
1aroLTYR 1046;LYS 1128
HIS 1017;HIS 1122;CYS 1130(Zinc binding)
 
1lbaATYR   46;LYS  128
HIS   17;HIS  122;CYS  130(Zinc binding)
mutant deletion 2-5, mutant A6K

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.4037
[8]p.836-838
[9]p.789-791
[10]Scheme 1, p.118-1193
[11]p.35435-35439

references
[1]
PubMed ID4582731
JournalJ Biol Chem
Year1973
Volume248
Pages7247-52
AuthorsInouye M, Arnheim N, Sternglanz R
TitleBacteriophage T7 lysozyme is an N-acetylmuramyl-L-alanine amidase.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND REVISION TO 118.
Medline ID94224877
PubMed ID8171031
JournalProc Natl Acad Sci U S A
Year1994
Volume91
Pages4034-8
AuthorsCheng X, Zhang X, Pflugrath JW, Studier FW
TitleThe structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase.
Related PDB1lba
Related UniProtKBP00806
[3]
PubMed ID9405156
JournalJ Mol Biol
Year1997
Volume274
Pages748-56
AuthorsJeruzalmi D, Steitz TA
TitleUse of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF COMPLEX WITH POLYMERASE.
Medline ID98336199
PubMed ID9670025
JournalEMBO J
Year1998
Volume17
Pages4101-13
AuthorsJeruzalmi D, Steitz TA
TitleStructure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
Related PDB1aro
Related UniProtKBP00806
[5]
PubMed ID9719635
JournalJ Mol Biol
Year1998
Volume281
Pages793-802
AuthorsVillemain J, Sousa R
TitleSpecificity in transcriptional regulation in the absence of specific DNA binding sites: the case of T7 lysozyme.
[6]
PubMed ID10543943
JournalJ Mol Biol
Year1999
Volume293
Pages457-75
AuthorsHuang J, Villemain J, Padilla R, Sousa R
TitleMechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase during different phases of transcription.
[7]
PubMed ID10679468
JournalCurr Opin Struct Biol
Year2000
Volume10
Pages117-23
AuthorsCheetham GM, Steitz TA
TitleInsights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases.
[8]
PubMed ID12654266
JournalJ Mol Biol
Year2003
Volume327
Pages833-42
AuthorsLiepinsh E, Genereux C, Dehareng D, Joris B, Otting G
TitleNMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.
Related PDB1iya,1j2s
[9]
PubMed ID12845326
JournalNat Immunol
Year2003
Volume4
Pages787-93
AuthorsKim MS, Byun M, Oh BH
TitleCrystal structure of peptidoglycan recognition protein LB from Drosophila melanogaster.
Related PDB1oht
[10]
PubMed ID14507260
JournalBiochem J
Year2004
Volume377
Pages111-20
AuthorsGenereux C, Dehareng D, Devreese B, Van Beeumen J, Frere JM, Joris B
TitleMutational analysis of the catalytic centre of the Citrobacter freundii AmpD N-acetylmuramyl-L-alanine amidase.
[11]
PubMed ID16103125
JournalJ Biol Chem
Year2005
Volume280
Pages35433-9
AuthorsLow LY, Yang C, Perego M, Osterman A, Liddington RC
TitleStructure and lytic activity of a Bacillus anthracis prophage endolysin.

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.

createdupdated
2004-05-112009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.