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
P49370	HUGA_VESVU	Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.		Secreted.
Q08169	HUGA_APIME	Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.	Homotetramer.	Secreted.@

KEGG Pathways
Map code	Pathways	E.C.
MAP00531	Glycosaminoglycan degradation
MAP01032	Glycan structures - 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 15377
PubChem					22247451 962 22247451 962

2atmA00	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1fcqA00	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1fcuA00	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1fcvA00	Unbound	Unbound	Unbound	Unbound		Bound:GCU-NAG-GCU-NAG-GCU	Unbound	Unbound	Unbound	Unbound
2j88A00	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	ASP 107;GLU 109;TYR 223
1fcqA00	ASP 111;GLU 113;TYR 227
1fcuA00	ASP 111;GLU 113;TYR 227
1fcvA00	ASP 111;GLU 113;TYR 227
2j88A00	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.

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