DB code: D00804

RLCP classification 1.32.68230.73 : Hydrolysis
CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
2.-.-.- :
E.C. 3.2.1.35
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 S00217 S00218 S00219 S00532 S00198 S00220 S00745 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 D00863 T00089

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq CAZy Pfam
Q12794 Hyaluronidase-1
Hyal-1
EC 3.2.1.35
Hyaluronoglucosaminidase-1
Lung carcinoma protein 1
LuCa-1
NP_149349.2 (Protein)
NM_033159.3 (DNA/RNA sequence)
NP_695013.1 (Protein)
NM_153281.1 (DNA/RNA sequence)
NP_695014.1 (Protein)
NM_153282.2 (DNA/RNA sequence)
NP_695015.1 (Protein)
NM_153283.2 (DNA/RNA sequence)
NP_695017.1 (Protein)
NM_153285.2 (DNA/RNA sequence)
GH56 (Glycoside Hydrolase Family 56)
PF01630 (Glyco_hydro_56)
[Graphical View]

KEGG enzyme name
Hyaluronoglucosaminidase
Hyaluronidase
Hyaluronoglucosidase
Chondroitinase
Chondroitinase I

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q12794 HYAL1_HUMAN Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate. Secreted. Lysosome.

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,carboxyl group,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,carboxyl group,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
2pe4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2pe4A02 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 [8], [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2pe4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 129;GLU 131;TYR 247
2pe4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
Fig.1 p.7955
[7]
Fig.6, p. 234-235
[8]
Fig.6 p.832-833
[9]
p.6914

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 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
[3]
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
[4]
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
[5]
Resource
Comments
Medline ID
PubMed ID 10907797
Journal Crit Rev Biochem Mol Biol
Year 2000
Volume 35
Pages 221-51
Authors Jedrzejas MJ
Title Structural and functional comparison of polysaccharide-degrading enzymes.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 11731267
Journal Matrix Biol
Year 2001
Volume 20
Pages 499-508
Authors Csoka AB, Frost GI, Stern R
Title The six hyaluronidase-like genes in the human and mouse genomes.
Related PDB
Related UniProtKB
[7]
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
[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 CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 20-435; MASS SPECTROMETRY, GLYCOSYLATION AT ASN-99; ASN-216 AND ASN-350, AND DISULFIDE BONDS.
Medline ID
PubMed ID 17503783
Journal Biochemistry
Year 2007
Volume 46
Pages 6911-20
Authors Chao KL, Muthukumar L, Herzberg O
Title Structure of human hyaluronidase-1, a hyaluronan hydrolyzing enzyme involved in tumor growth and angiogenesis.
Related PDB 2pe4
Related UniProtKB Q12794
[10]
Resource
Comments
Medline ID
PubMed ID 17602139
Journal Glycobiology
Year 2007
Volume 17
Pages 963-71
Authors Hofinger ES, Bernhardt G, Buschauer A
Title Kinetics of Hyal-1 and PH-20 hyaluronidases: comparison of minimal substrates and analysis of the transglycosylation reaction.
Related PDB
Related UniProtKB
[11]
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
[12]
Resource
Comments
Medline ID
PubMed ID 17620008
Journal Glycoconj J
Year 2008
Volume 25
Pages 101-9
Authors Hofinger ES, Hoechstetter J, Oettl M, Bernhardt G, Buschauer A
Title Isoenzyme-specific differences in the degradation of hyaluronic acid by mammalian-type hyaluronidases.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-56 with a retaining mechanism.
According to the literature [5], this enzyme hydrolyzes beta-N-acetyl-hexosamine-(1->4) glycosidic bonds in chondroitin and chondroitin-suflate as well as in hyarulonan.
According to the literature [4], [7], [8] and [9], this enzyme catalyzes the following reaction:
(0) Asp 129 may modulate the pKa of Glu131. On the other hand, the nucleophile, N-acetyl group of substrate can be modulated by Asp129 and Tyr247 (see [4]). 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) Glu131 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
2008-07-28 2011-12-22