DB code: M00026

RLCP classification 1.32.68200.2 : Hydrolysis
CATH domain 2.60.40.290 : Immunoglobulin-like
3.30.379.10 : Chitobiase; domain 2
3.20.20.80 : TIM Barrel Catalytic domain
2.60.40.320 : Immunoglobulin-like
E.C. 3.2.1.52
CSA 1qba
M-CSA 1qba
MACiE

CATH domain Related DB codes (homologues)
2.60.40.290 : Immunoglobulin-like M00219 D00479 D00502 D00504 M00192
2.60.40.320 : Immunoglobulin-like T00066
3.20.20.80 : TIM Barrel S00202 S00210 S00748 S00906 S00907 S00911 S00912 S00915 M00134 M00160 D00479 S00204 S00205 S00206 S00207 S00203 S00208 S00209 S00211 S00213 S00214 M00113 T00307 D00165 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00112 M00193 M00346 T00057 T00062 T00063 T00066 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
Q54468 Chitobiase
EC 3.2.1.52
N-acetyl-beta-glucosaminidase
Beta-N-acetylhexosaminidase
GH20 (Glycoside Hydrolase Family 20)
PF03173 (CHB_HEX)
PF03174 (CHB_HEX_C)
PF00728 (Glyco_hydro_20)
PF02838 (Glyco_hydro_20b)
[Graphical View]

KEGG enzyme name
beta-N-Acetylhexosaminidase
Hexosaminidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q54468 CHB_SERMA hydrolysis of terminal non-reducing n-acetyl- d-hexosamine residues in n-acetyl-beta-d-hexosaminides. monomer. periplasmic.

KEGG Pathways
Map code Pathways E.C.
MAP00511 N-Glycan degradation
MAP00520 Nucleotide sugars metabolism
MAP00530 Aminosugars metabolism
MAP00531 Glycosaminoglycan degradation
MAP00603 Glycosphingolipid biosynthesis - globoseries
MAP00604 Glycosphingolipid biosynthesis - ganglioseries

Compound table
Substrates Products Intermediates
KEGG-id C03879 C00001 C01674 C03518 C02848 C03136 C00140 C01132
E.C.
Compound N-Acetyl-beta-D-hexosaminide H2O Chitobiose N-Acetyl-D-glucosaminide N-Acetyl-D-galactosaminide N-Acetyl-D-hexosamine N-Acetyl-D-glucosamine N-Acetyl-D-galactosamine
Type amide group,carbohydrate H2O amide group,polysaccharide amide group,carbohydrate amide group,carbohydrate amide group,carbohydrate amide group,carbohydrate amide group,carbohydrate
ChEBI 15377
28681
21601
506227
28037
PubChem 962
22247451
439544
439916
439174
35717
1c7sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1c7tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbbA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1c7sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1c7tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbbA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1c7sA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:CBS Unbound Unbound Unbound Unbound Unbound
1c7tA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:CBS Unbound Unbound Unbound Unbound Unbound
1qbaA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbbA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:CBS Unbound Unbound Unbound Unbound Unbound
1c7sA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1c7tA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbaA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qbbA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c7sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c7tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qbaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qbbA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c7sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c7tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qbaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qbbA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c7sA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;GLU 540 mutant D539A
1c7tA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 539; mutant E540D
1qbaA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 539;GLU 540
1qbbA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 539;GLU 540
1c7sA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c7tA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qbaA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qbbA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.191-192
[6]
p.642-643
[7]
Scheme 1, p.948
[10]
p.613-614

References
[1]
Resource
Comments
Medline ID
PubMed ID 2510544
Journal Anal Biochem
Year 1989
Volume 180
Pages 195-204
Authors Maley F, Trimble RB, Tarentino AL, Plummer TH Jr
Title Characterization of glycoproteins and their associated oligosaccharides through the use of endoglycosidases.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1840099
Journal Dev Neurosci
Year 1991
Volume 13
Pages 288-94
Authors Suzuki K, Vanier MT
Title Biochemical and molecular aspects of late-onset GM2-gangliosidosis: B1 variant as a prototype.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1453472
Journal J Mol Biol
Year 1992
Volume 228
Pages 696-7
Authors Tews I, Dauter Z, Oppenheim AB, Vorgias CE
Title Crystallization of recombinant chitobiase from Serratia marcescens.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8958090
Journal Ann N Y Acad Sci
Year 1996
Volume 799
Pages 190-2
Authors Vorgias CE, Perrakis A, Tews I
Title Structure-function studies on the chitinolytic enzymes of Serratia marcescens chitinase and chitobiase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8621090
Journal Gene
Year 1996
Volume 170
Pages 63-7
Authors Tews I, Vincentelli R, Vorgias CE
Title N-Acetylglucosaminidase (chitobiase) from Serratia marcescens: gene sequence, and protein production and purification in Escherichia coli.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID 96266355
PubMed ID 8673609
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 638-48
Authors Tews I, Perrakis A, Oppenheim A, Dauter Z, Wilson KS, Vorgias CE
Title Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.
Related PDB 1qba 1qbb
Related UniProtKB Q54468
[7]
Resource
Comments
Medline ID
PubMed ID 9396742
Journal Biochem J
Year 1997
Volume 328
Pages 945-9
Authors Drouillard S, Armand S, Davies GJ, Vorgias CE, Henrissat B
Title Serratia marcescens chitobiase is a retaining glycosidase utilizing substrate acetamido group participation.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10698282
Journal Acta Biochim Pol
Year 1999
Volume 46
Pages 739-51
Authors Zwierz K, Zalewska A, Zoch-Zwierz A
Title Isoenzymes of N-acetyl-beta-hexosaminidase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10513893
Journal Biosci Rep
Year 1999
Volume 19
Pages 163-8
Authors Sonnino S, Brocca P, Acquotti D, Bernardi A, Raimondi L, Kiso M, Ishida H, Li SC, Li YT
Title The structural basis for the susceptibility of gangliosides to enzymatic degradation.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10884356
Journal J Mol Biol
Year 2000
Volume 300
Pages 611-7
Authors Prag G, Papanikolau Y, Tavlas G, Vorgias CE, Petratos K, Oppenheim AB
Title Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540.
Related PDB 1c7s 1c7t
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11785767
Journal Curr Opin Struct Biol
Year 2001
Volume 11
Pages 635-43
Authors Kogelberg H, Feizi T
Title New structural insights into lectin-type proteins of the immune system.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-20. This enzyme has a retaining mechanism.
According to the literature [6], [7] and [10], the reaction of this enzyme proceeds as follows:
(0) Asp539 might modulate the general acid, Glu540, by restraining the positioning of Glu540.
(1) Glu540 acts as a general acid, to protonate the glycosidic oxygen atom, the O1 atom, leading to the transition state with oxocarbenium ion character.
(2) Asp 539 modulate the N-acetyl group of the substrate, by forming a hydrogen bond with the N2 atom of the N-acetyl group. The O7 oxygen atom of the N-acetyl group makes a nucleophilic attack on the C1 atom of the transition state. This nucleophilic substitution seems to be S1-like reaction.
(3) A covalent cyclic oxazolinium ion intermediate is formed and stabilized by Asp539, which forms a hydrogen bond with the N2 atom.
(4) A water, which is activated by a general base, Glu540, makes a nucleophilic attack on the C1 atom of the intermediate, leading again to the transition state with oxocarbenium ion character.
(5) The covalent bond between the C1 atom and the O7 oxygen atom is broken, and finally the product is formed.
Thus, Asp539 play multiple roles, a stabilizer for the oxazolinium ion intermediate, and modulators for the N-acetamido group and Glu540 (see [10]).

Created Updated
2009-07-17 2009-07-17