EzCatDB: S00520
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00520
RLCP classification1.30.4950.1 : Hydrolysis
CATH domainDomain 11.10.530.10 : LysozymeCatalytic domain
E.C.3.2.1.17

CATH domainRelated DB codes (homologues)
1.10.530.10 : LysozymeD00170,S00509

Enzyme Name
UniProtKBKEGG

P00718
Protein nameLysozyme glysozyme
muramidase
globulin G
mucopeptide glucohydrolase
globulin G1
N,O-diacetylmuramidase
lysozyme g
L-7001
1,4-N-acetylmuramidase
mucopeptide N-acetylmuramoylhydrolase
PR1-lysozyme
SynonymsEC 3.2.1.17
1,4-beta-N-acetylmuramidase
Goose-type lysozyme
PfamPF01464 (SLT)
[Graphical view]
CAZyGH23 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberP00718
Entry nameLYG_ANSAN
ActivityHydrolysis of (1->4)-beta-linkages between N- acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins.
Subunit
Subcellular locationSecreted.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00889C00851C00001C04394C00851C00140
CompoundPeptidoglycanChitodextrinH2OPeptidoglycan(N-acetyl-D-glucosamine)ChitodextrinN-Acetyl-D-glucosamine
Typeamino acids,amide group,amine group,carbohydrate,peptide/protein,polysaccharideamide group,polysaccharideH2Oamino acids,amide group,amine group,carbohydrate,lipid,peptide/protein,polysaccharideamide group,polysaccharideamide group,carbohydrate
ChEBI

15377
8006

506227
PubChem

962
22247451
5462260

439174
              
153lAUnboundUnbound UnboundUnboundUnbound
154lAUnboundUnbound UnboundBound:NAG-NAG-NAGUnbound

Active-site residues
resource
literature [4]
pdbCatalytic residues
         
153lAGLU 73
154lAGLU 73

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.64-65
[5]p.214-218

references
[1]
PubMed ID6866082
JournalNature
Year1983
Volume303
Pages828-31
AuthorsGrutter MG, Weaver LH, Matthews BW
TitleGoose lysozyme structure: an evolutionary link between hen and bacteriophage lysozymes?
[2]
PubMed ID6442995
JournalJ Mol Evol
Year1984
Volume21
Pages97-111
AuthorsWeaver LH, Grutter MG, Remington SJ, Gray TM, Isaacs NW, Matthews BW
TitleComparison of goose-type, chicken-type, and phage-type lysozymes illustrates the changes that occur in both amino acid sequence and three-dimensional structure during evolution.
[3]
PubMed ID4062692
JournalAust J Biol Sci
Year1985
Volume38
Pages13-22
AuthorsIsaacs NW, Machin KJ, Masakuni M
TitleThree-dimensional structure of goose-type lysozyme from the egg white of the Australian black swan, Cygnus atratus.
[4]
CommentsX-ray crystallography
PubMed ID7823320
JournalJ Mol Biol
Year1995
Volume245
Pages54-68
AuthorsWeaver LH, Grutter MG, Matthews BW
TitleThe refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue.
Related PDB153l,154l
[5]
PubMed ID8765301
JournalEXS
Year1996
Volume75
Pages185-222
AuthorsStrynadka NC, James MN
TitleLysozyme: a model enzyme in protein crystallography.
[6]
PubMed ID8564539
JournalNat Struct Biol
Year1996
Volume3
Pages133-40
AuthorsMonzingo AF, Marcotte EM, Hart PJ, Robertus JD
TitleChitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core.
[7]
PubMed ID9774706
JournalBiochim Biophys Acta
Year1998
Volume1388
Pages53-65
AuthorsHonda Y, Fukamizo T
TitleSubstrate binding subsites of chitinase from barley seeds and lysozyme from goose egg white.
[8]
PubMed ID12369923
JournalCurr Protein Pept Sci
Year2000
Volume1
Pages105-24
AuthorsFukamizo T
TitleChitinolytic enzymes: catalysis, substrate binding, and their application.
[9]
PubMed ID11866097
JournalBiosci Biotechnol Biochem
Year2002
Volume66
Pages147-56
AuthorsThammasirirak S, Torikata T, Takami K, Murata K, Araki T
TitleThe primary structure of cassowary (Casuarius casuarius) goose type lysozyme.

comments
This enzyme belongs to the glycosidase family-23.
Although either Asp86 or Asp97 has been annotated as a counterpart to Asp52 of hen egg white lysozyme (S00509 in EzCatDB), the exact position is distant from that of the couterpart, suggesting that the second acidic residue, involved in catalysis, is not important in this enzyme (see [4]).
The paper [4] ruled out the possibility of a double displacement mechanism for this enzyme, since the second catalytic residue, acting as the nucleophile, is not essential. Taken together, the catalytic reaction probably proceeds as follows:
(1) Glu73 acts as a general acid, to protonates the glycosidic oxygen of the scissile bond, leading to the formation of an oxocarbonium ion intermediate.
(2) The sidechain of Glu73 acts as a stabilizer, which stabilizes the oxocarbonium ion intermediate, and also acts as a general base, which activates a nearby water.
(3) Finally, the activated water makes a nucleophilic attack on the intermediate to complete the hydrolysis reaction.

createdupdated
2004-11-302009-02-26
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.