DB code: S00745

RLCP classification 1.32.68230.73 : Hydrolysis
CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 3.2.1.35
CSA 1fcq
M-CSA 1fcq
MACiE

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 S00217 S00218 S00219 S00532 S00198 S00220 S00537 S00538 S00539 S00826 S00841 S00235 S00239 S00240 S00243 S00244 S00199 S00200 S00201 S00221 S00222 S00847 S00224 S00225 S00226 D00014 D00029 M00141 T00015 T00239 D00664 D00665 D00804 D00863 T00089

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam RefSeq
P49370 Hyaluronidase A (Hya A) (EC 3.2.1.35) (Hyaluronoglucosaminidase A) (Allergen Ves v II)AltName: Allergen=Ves v 2a;
None GH56 (Glycoside Hydrolase Family 56)
PF01630 (Glyco_hydro_56)
[Graphical View]
Q08169 Hyaluronidase (Hya) (EC 3.2.1.35) (Hyaluronoglucosaminidase) (Allergen Api m II)AltName: Allergen=Api m 2;
None GH56 (Glycoside Hydrolase Family 56)
PF01630 (Glyco_hydro_56)
[Graphical View]
NP_001011619.1 (Protein)
NM_001011619.1 (DNA/RNA sequence)

KEGG enzyme name
Hyaluronoglucosaminidase
Hyaluronidase
Hyaluronoglucosidase
Chondroitinase
Chondroitinase I

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q08169 HUGA_APIME Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate. Homotetramer. Secreted.@
P49370 HUGA_VESVU Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate. Secreted.

KEGG Pathways
Map code Pathways E.C.
MAP01032 Glycan structures - degradation
MAP00531 Glycosaminoglycan degradation

Compound table
Substrates Products Intermediates
KEGG-id C00518 C00401 C00634 C00635 C00001 C00518 C00401 C00634 C00635 I00111
E.C.
Compound Hyaluronate Chondroitin Chondroitin 4-sulfate Chondroitin 6-sulfate H2O Hyaluronate Chondroitin Chondroitin 4-sulfate Chondroitin 6-sulfate Intramolecular cyclic intermediate at reducing end of hyaluronate
Type amide group,carbohydrate,polysaccharide amide group,carbohydrate,carboxyl group,polysaccharide amide group,carbohydrate,carboxyl group,polysaccharide,sulfate group amide group,carbohydrate,carboxyl group,polysaccharide,sulfate group H2O amide group,carbohydrate,polysaccharide amide group,carbohydrate,carboxyl group,polysaccharide amide group,carbohydrate,carboxyl group,polysaccharide,sulfate group amide group,carbohydrate,carboxyl group,polysaccharide,sulfate group
ChEBI 15377
PubChem 962
22247451
2atmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fcqA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fcuA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fcvA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:GCU-NAG-GCU-NAG-GCU Unbound Unbound Unbound Unbound
2j88A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [5], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2atmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 107;GLU 109;TYR 223
1fcqA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 111;GLU 113;TYR 227
1fcuA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 111;GLU 113;TYR 227
1fcvA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 111;GLU 113;TYR 227
2j88A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 111;GLU 113;TYR 227

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.1, p. 7955
[5]
Fig.3, Fig.6, Fig.7, p. 1029-1030
[6]
Fig.6, p.235
[8]
Fig.6, p. 832-833

References
[1]
Resource
Comments
Medline ID
PubMed ID 8687420
Journal Biochem J
Year 1996
Volume 316
Pages 695-6
Authors Henrissat B, Bairoch A
Title Updating the sequence-based classification of glycosyl hydrolases.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8952478
Journal Biochemistry
Year 1996
Volume 35
Pages 15280-7
Authors Sulzenbacher G, Driguez H, Henrissat B, Schulein M, Davies GJ
Title Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9288901
Journal Eur J Biochem
Year 1997
Volume 247
Pages 810-4
Authors Arming S, Strobl B, Wechselberger C, Kreil G
Title In vitro mutagenesis of PH-20 hyaluronidase from human sperm.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 1997
Volume 119
Pages 7954-59
Authors Tews I, vanScheltinga ACT, Perrakis A, Wilson KS, Dijkstra BW
Title Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 42-362, AND ACTIVE SITE.
Medline ID
PubMed ID 11080624
Journal Structure
Year 2000
Volume 8
Pages 1025-35
Authors Markovic-Housley Z, Miglierini G, Soldatova L, Rizkallah PJ, Muller U, Schirmer T
Title Crystal structure of hyaluronidase, a major allergen of bee venom.
Related PDB 1fcq 1fcu 1fcv
Related UniProtKB Q08169
[6]
Resource
Comments
Medline ID
PubMed ID 16104017
Journal Proteins
Year 2005
Volume 61
Pages 227-38
Authors Jedrzejas MJ, Stern R
Title Structures of vertebrate hyaluronidases and their unique enzymatic mechanism of hydrolysis.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-331, PARTIAL PROTEIN SEQUENCE, MASS SPECTROMETRY, GLYCOSYLATION AT ASN-79; ASN-99 AND ASN-127, AND DISULFIDE BONDS.
Medline ID
PubMed ID 16699186
Journal Acta Crystallogr D Biol Crystallogr
Year 2006
Volume 62
Pages 595-604
Authors Skov LK, Seppala U, Coen JJ, Crickmore N, King TP, Monsalve R, Kastrup JS, Spangfort MD, Gajhede M
Title Structure of recombinant Ves v 2 at 2.0 Angstrom resolution: structural analysis of an allergenic hyaluronidase from wasp venom.
Related PDB 2atm
Related UniProtKB P49370
[8]
Resource
Comments
Medline ID
PubMed ID 16522010
Journal Chem Rev
Year 2006
Volume 106
Pages 818-39
Authors Stern R, Jedrzejas MJ
Title Hyaluronidases: their genomics, structures, and mechanisms of action.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY DIFFRACTION
Medline ID
PubMed ID 17374540
Journal J Mol Biol
Year 2007
Volume 368
Pages 742-52
Authors Padavattan S, Schirmer T, Schmidt M, Akdis C, Valenta R, Mittermann I, Soldatova L, Slater J, Mueller U, Markovic-Housley Z
Title Identification of a B-cell epitope of hyaluronidase, a major bee venom allergen, from its crystal structure in complex with a specific Fab.
Related PDB 2j88
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 17408700
Journal Life Sci
Year 2007
Volume 80
Pages 1921-43
Authors Girish KS, Kemparaju K
Title The magic glue hyaluronan and its eraser hyaluronidase: a biological overview.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-56 with a retaining mechanism.
This enzyme hydrolyzes beta-N-acetyl-hexosamine-(1->4) glycosidic bonds in chondroitin and chondroitin-suflate as well as in hyarulonan (see ref.[5] of D00804 in EzCatDB).
According to the literature [4], [5], [6] and [8], this enzyme catalyzes the following reaction:
(0) Asp 111 (of 1fcv) may modulate the pKa of Glu113. On the other hand, the nucleophile, N-acetyl group of substrate can be modulated by Asp111 and Tyr227 (see [5]). Moreover, the interaction of the nucleophilic N-acetyl group with these residues may induce the deformation of the sugar ring from chair to distorted boat conformation, which facilitate the formation of oxocarbonium ion transtion-state (SN1-like reaction).
(1) The carbonyl oxygen of the N-acetyl group makes a nucleophilic attack on the C1 atom of the same sugar unit, to form an intramolecular covalent intermediate. At the same time, Glu131 acts as a general acid to protonate the leaving glycan on the reducing side of the glycosidic bond to be cleaved. Thus, the glycosidic bond in the substrate on the non-reducing side of the bond is cleaved, resulting in the inversion of the anomeric C1 atom configuration.
(2) Glu113 acts as a general base to activate a water molecule.
(3) The activated water makes a nucleophilic attack on the C1 atom of the intermediate, resulting in the second inversion of the C1 configuration. Thus, the reaction completes.

Created Updated
2008-07-29 2011-12-26