EzCatDB: S00536
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DB codeS00536
RLCP classification1.13.11100.286 : Hydrolysis
CATH domainDomain 13.40.80.10 : Lysozyme-likeCatalytic domain
E.C.3.5.1.28

CATH domainRelated DB codes (homologues)
3.40.80.10 : Lysozyme-likeS00502,S00535

Enzyme Name
UniProtKBKEGG

Q8INK6
Protein namePeptidoglycan-recognition protein-LBN-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
RefSeqNP_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)
PfamPF01510 (Amidase_2)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00550Peptidoglycan biosynthesis

UniProtKB:Accession NumberQ8INK6
Entry namePGPLB_DROME
ActivityHydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
SubunitMonomer.
Subcellular locationIsoform C: Secreted (Potential).
CofactorBinds 1 zinc ion per subunit.

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


             
1ohtABound:_ZNUnbound UnboundUnbound

Active-site residues
resource
literature [9]
pdbCatalytic residuesCofactor-binding residues
          
1ohtATYR 78;HIS 43
HIS 42;HIS 152;CYS 160(Zinc binding)

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
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.

createdupdated
2004-05-112009-02-26


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