DB code: S00520

RLCP classification 1.30.4950.1 : Hydrolysis
CATH domain 1.10.530.10 : Lysozyme Catalytic domain
E.C. 3.2.1.17
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.530.10 : Lysozyme D00170 S00509

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
P00718 Lysozyme g
EC 3.2.1.17
1,4-beta-N-acetylmuramidase
Goose-type lysozyme
GH23 (Glycoside Hydrolase Family 23)
PF01464 (SLT)
[Graphical View]

KEGG enzyme name
lysozyme
muramidase
globulin G
mucopeptide glucohydrolase
globulin G1
N,O-diacetylmuramidase
lysozyme g
L-7001
1,4-N-acetylmuramidase
mucopeptide N-acetylmuramoylhydrolase
PR1-lysozyme

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00718 LYG_ANSAN Hydrolysis 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. Secreted.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00889 C00851 C00001 C04394 C00851 C00140
E.C.
Compound Peptidoglycan Chitodextrin H2O Peptidoglycan(N-acetyl-D-glucosamine) Chitodextrin N-Acetyl-D-glucosamine
Type amino acids,amide group,amine group,carbohydrate,peptide/protein,polysaccharide amide group,polysaccharide H2O amino acids,amide group,amine group,carbohydrate,lipid,peptide/protein,polysaccharide amide group,polysaccharide amide group,carbohydrate
ChEBI 15377
8006
506227
PubChem 962
22247451
5462260
439174
153lA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
154lA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAG-NAG-NAG Unbound

Reference for Active-site residues
resource references E.C.
literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
153lA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73
154lA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.64-65
[5]
p.214-218

References
[1]
Resource
Comments
Medline ID
PubMed ID 6866082
Journal Nature
Year 1983
Volume 303
Pages 828-31
Authors Grutter MG, Weaver LH, Matthews BW
Title Goose lysozyme structure: an evolutionary link between hen and bacteriophage lysozymes?
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6442995
Journal J Mol Evol
Year 1984
Volume 21
Pages 97-111
Authors Weaver LH, Grutter MG, Remington SJ, Gray TM, Isaacs NW, Matthews BW
Title Comparison 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.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 4062692
Journal Aust J Biol Sci
Year 1985
Volume 38
Pages 13-22
Authors Isaacs NW, Machin KJ, Masakuni M
Title Three-dimensional structure of goose-type lysozyme from the egg white of the Australian black swan, Cygnus atratus.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7823320
Journal J Mol Biol
Year 1995
Volume 245
Pages 54-68
Authors Weaver LH, Grutter MG, Matthews BW
Title The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue.
Related PDB 153l 154l
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8765301
Journal EXS
Year 1996
Volume 75
Pages 185-222
Authors Strynadka NC, James MN
Title Lysozyme: a model enzyme in protein crystallography.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8564539
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 133-40
Authors Monzingo AF, Marcotte EM, Hart PJ, Robertus JD
Title Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9774706
Journal Biochim Biophys Acta
Year 1998
Volume 1388
Pages 53-65
Authors Honda Y, Fukamizo T
Title Substrate binding subsites of chitinase from barley seeds and lysozyme from goose egg white.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 12369923
Journal Curr Protein Pept Sci
Year 2000
Volume 1
Pages 105-24
Authors Fukamizo T
Title Chitinolytic enzymes: catalysis, substrate binding, and their application.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11866097
Journal Biosci Biotechnol Biochem
Year 2002
Volume 66
Pages 147-56
Authors Thammasirirak S, Torikata T, Takami K, Murata K, Araki T
Title The primary structure of cassowary (Casuarius casuarius) goose type lysozyme.
Related PDB
Related UniProtKB

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.

Created Updated
2004-11-30 2009-02-26