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 29105		15377 15377
PubChem	32051 32051		22247451 962 22247451 962

1ohtA	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	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.

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