EzCatDB: M00026
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeM00026
RLCP classification1.32.68200.2 : Hydrolysis
CATH domainDomain 12.60.40.290 : Immunoglobulin-like
Domain 23.30.379.10 : Chitobiase; domain 2
Domain 33.20.20.80 : TIM BarrelCatalytic domain
Domain 42.60.40.320 : Immunoglobulin-like
E.C.3.2.1.52
CSA1qba

CATH domainRelated DB codes (homologues)
2.60.40.290 : Immunoglobulin-likeM00219,D00479,D00502,D00504,M00192
2.60.40.320 : Immunoglobulin-likeT00066
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

Q54468
Protein nameChitobiasebeta-N-Acetylhexosaminidase
Hexosaminidase
SynonymsEC 3.2.1.52
N-acetyl-beta-glucosaminidase
Beta-N-acetylhexosaminidase
PfamPF03173 (CHB_HEX)
PF03174 (CHB_HEX_C)
PF00728 (Glyco_hydro_20)
PF02838 (Glyco_hydro_20b)
[Graphical view]
CAZyGH20 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00511N-Glycan degradation
MAP00520Nucleotide sugars metabolism
MAP00530Aminosugars metabolism
MAP00531Glycosaminoglycan degradation
MAP00603Glycosphingolipid biosynthesis - globoseries
MAP00604Glycosphingolipid biosynthesis - ganglioseries

UniProtKB:Accession NumberQ54468
Entry nameCHB_SERMA
Activityhydrolysis of terminal non-reducing n-acetyl- d-hexosamine residues in n-acetyl-beta-d-hexosaminides.
Subunitmonomer.
Subcellular locationperiplasmic.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC03879C00001C01674C03518C02848C03136C00140C01132
CompoundN-Acetyl-beta-D-hexosaminideH2OChitobioseN-Acetyl-D-glucosaminideN-Acetyl-D-galactosaminideN-Acetyl-D-hexosamineN-Acetyl-D-glucosamineN-Acetyl-D-galactosamine
Typeamide group,carbohydrateH2Oamide group,polysaccharideamide group,carbohydrateamide group,carbohydrateamide group,carbohydrateamide group,carbohydrateamide group,carbohydrate
ChEBI
15377
28681


21601
506227
28037
PubChem
962
22247451
439544


439916
439174
35717
                
1c7sA01Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1c7tA01Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbaA01Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbbA01Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1c7sA02Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1c7tA02Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbaA02Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbbA02Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1c7sA03Unbound Bound:CBSUnboundUnboundUnboundUnboundUnbound
1c7tA03Unbound Bound:CBSUnboundUnboundUnboundUnboundUnbound
1qbaA03Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbbA03Unbound Bound:CBSUnboundUnboundUnboundUnboundUnbound
1c7sA04Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1c7tA04Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbaA04Unbound UnboundUnboundUnboundUnboundUnboundUnbound
1qbbA04Unbound UnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residuescomment
          
1c7sA01 
 
1c7tA01 
 
1qbaA01 
 
1qbbA01 
 
1c7sA02 
 
1c7tA02 
 
1qbaA02 
 
1qbbA02 
 
1c7sA03       ;GLU 540
mutant D539A
1c7tA03ASP 539;       
mutant E540D
1qbaA03ASP 539;GLU 540
 
1qbbA03ASP 539;GLU 540
 
1c7sA04 
 
1c7tA04 
 
1qbaA04 
 
1qbbA04 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.191-192
[6]p.642-643
[7]Scheme 1, p.948
[10]p.613-614

references
[1]
PubMed ID2510544
JournalAnal Biochem
Year1989
Volume180
Pages195-204
AuthorsMaley F, Trimble RB, Tarentino AL, Plummer TH Jr
TitleCharacterization of glycoproteins and their associated oligosaccharides through the use of endoglycosidases.
[2]
PubMed ID1840099
JournalDev Neurosci
Year1991
Volume13
Pages288-94
AuthorsSuzuki K, Vanier MT
TitleBiochemical and molecular aspects of late-onset GM2-gangliosidosis: B1 variant as a prototype.
[3]
PubMed ID1453472
JournalJ Mol Biol
Year1992
Volume228
Pages696-7
AuthorsTews I, Dauter Z, Oppenheim AB, Vorgias CE
TitleCrystallization of recombinant chitobiase from Serratia marcescens.
[4]
PubMed ID8958090
JournalAnn N Y Acad Sci
Year1996
Volume799
Pages190-2
AuthorsVorgias CE, Perrakis A, Tews I
TitleStructure-function studies on the chitinolytic enzymes of Serratia marcescens chitinase and chitobiase.
[5]
PubMed ID8621090
JournalGene
Year1996
Volume170
Pages63-7
AuthorsTews I, Vincentelli R, Vorgias CE
TitleN-Acetylglucosaminidase (chitobiase) from Serratia marcescens: gene sequence, and protein production and purification in Escherichia coli.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID96266355
PubMed ID8673609
JournalNat Struct Biol
Year1996
Volume3
Pages638-48
AuthorsTews I, Perrakis A, Oppenheim A, Dauter Z, Wilson KS, Vorgias CE
TitleBacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.
Related PDB1qba,1qbb
Related UniProtKBQ54468
[7]
PubMed ID9396742
JournalBiochem J
Year1997
Volume328
Pages945-9
AuthorsDrouillard S, Armand S, Davies GJ, Vorgias CE, Henrissat B
TitleSerratia marcescens chitobiase is a retaining glycosidase utilizing substrate acetamido group participation.
[8]
PubMed ID10698282
JournalActa Biochim Pol
Year1999
Volume46
Pages739-51
AuthorsZwierz K, Zalewska A, Zoch-Zwierz A
TitleIsoenzymes of N-acetyl-beta-hexosaminidase.
[9]
PubMed ID10513893
JournalBiosci Rep
Year1999
Volume19
Pages163-8
AuthorsSonnino S, Brocca P, Acquotti D, Bernardi A, Raimondi L, Kiso M, Ishida H, Li SC, Li YT
TitleThe structural basis for the susceptibility of gangliosides to enzymatic degradation.
[10]
CommentsX-ray crystallography
PubMed ID10884356
JournalJ Mol Biol
Year2000
Volume300
Pages611-7
AuthorsPrag G, Papanikolau Y, Tavlas G, Vorgias CE, Petratos K, Oppenheim AB
TitleStructures 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 PDB1c7s,1c7t
[11]
PubMed ID11785767
JournalCurr Opin Struct Biol
Year2001
Volume11
Pages635-43
AuthorsKogelberg H, Feizi T
TitleNew structural insights into lectin-type proteins of the immune system.

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]).

createdupdated
2009-07-172009-07-17


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.