EzCatDB: T00065

DB codeT00065
RLCP classification1.31.36210.99
CATH domainDomain 12.120.10.10Catalytic domain
Domain 22.60.40.10
Domain 32.60.120.260
E.C.3.2.1.18
CSA1euu

CATH domainRelated DB codes (homologues)
2.120.10.10D00173,M00310,T00064,T00208
2.60.120.260M00124,T00005,T00066
2.60.40.10M00131,T00257,T00005,M00113,M00127,M00132,M00323,M00325,M00327,M00329,M00330,M00331,M00332,T00307,D00166,D00500,M00112,M00193,T00063,T00067,T00245

Enzyme Name
Swiss-protKEGG

Q02834
Protein nameSialidaseexo-alpha-sialidase
neuraminidase
sialidase
alpha-neuraminidase
acetylneuraminidase
SynonymsEC 3.2.1.18
Neuraminidase

KEGG pathways
MAP codePathways
MAP00511N-Glycan degradation
MAP00600Sphingolipid metabolism
MAP01032Glycan structures - degradation

Swiss-prot:Accession NumberQ02834
Entry nameNANH_MICVI
ActivityHydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Subunit
Subcellular locationSecreted.
Cofactor


CofactorsSubstratesProductsintermediates
KEGG-idC01330C04730C06128C04884C04927C06139C06140C00001C00270C01290C02686C06135C04911C06140C06141
CompoundSodiumGM3N-Acetylneuraminyl-galactosylceramideN-Acetyl-D-galactosaminyl-(N-acetylneuraminyl)-D-galactosyl-D-glucosylceramideN-Acetylneuraminyl-D-galactosyl-N-acetyl-D-galactosaminyl-(N- acetylneuraminyl)-D-galactosyl-D-glucosylceramideGQ1GT1bH2ON-Acetylneuraminatebeta-D-Galactosyl-1,4-beta-D-glucosylceramideGalactosylceramideGA2D-Galactosyl-N-acetyl-D-galactosaminyl-(N-acetylneuraminyl)-D-galactosyl-D-glucosylceramideGT1bGD1bOxocarbenium-ion-like transition-state
Typeunivalent metal (Na+, K+)amide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideH2Oamide group,carbohydrate,carboxyl groupamide group,carbohydrate,lipid,polysaccharideamide group,carbohydrate,lipidamide group,carbohydrate,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharideamide group,carbohydrate,carboxyl group,lipid,polysaccharide
1eurAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eusAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundTransition-state-analogue:DAN
1eutA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1euuA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1w8nA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundTransition-state-analogue:DAN
1w8oA01UnboundUnboundUnboundUnboundUnboundUnboundAnalogue:CIT
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2berA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
Analogue:SLBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9A01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9B01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9C01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eutA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1euuA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1w8nA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1w8oA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2berA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9A02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9B02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9C02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eutA03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1euuA03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1w8nA03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1w8oA03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2berA03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9A03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9B03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2bq9C03Bound:_NAUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;Q02834 & literature [3], [7], [8]
pdbCatalytic residuescomment
1eurAASP 92;GLU 260;TYR 370

1eusAASP 92;GLU 260;TYR 370

1eutA01ASP 92;GLU 260;TYR 370

1euuA01ASP 92;GLU 260;TYR 370

1w8nA01      ;GLU 260;TYR 370
mutant D92G
1w8oA01      ;GLU 260;TYR 370
mutant D92G
2berA01ASP 92;GLU 260;       
mutant Y370G
2bq9A01ASP 92;       ;TYR 370
mutant E260A
2bq9B01ASP 92;       ;TYR 370
mutant E260A
2bq9C01ASP 92;       ;TYR 370
mutant E260A
1eutA02

1euuA02

1w8nA02

1w8oA02

2berA02

2bq9A02

2bq9B02

2bq9C02

1eutA03

1euuA03

1w8nA03

1w8oA03

2berA03

2bq9A03

2bq9B03

2bq9C03


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.1199
[7]p.12682, Scheme 2, p.12687-12689
[8]


references
[1]
PubMed ID1613796
JournalJ Mol Biol
Year1992
Volume225
Pages1135-6
AuthorsTaylor G, Dineley L, Glowka M, Laver G
TitleCrystallization and preliminary crystallographic study of neuraminidase from Micromonospora viridifaciens.
[2]
PubMed ID7981969
JournalTrends Microbiol
Year1994
Volume2
Pages271-7
AuthorsVimr ER
TitleMicrobial sialidases: does bigger always mean better?
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID96164436
PubMed ID8591030
JournalStructure
Year1995
Volume3
Pages1197-205
AuthorsGaskell A, Crennell S, Taylor G
TitleThe three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
Related PDB1eur,1eus,1eut,1euu
Related Swiss-protQ02834
[4]
PubMed ID8994884
JournalCurr Opin Struct Biol
Year1996
Volume6
Pages830-7
AuthorsTaylor G
TitleSialidases: structures, biological significance and therapeutic potential.
[5]
PubMed ID9147054
JournalGlycobiology
Year1997
Volume7
Pages445-51
AuthorsSmith LE, Eichinger D
TitleDirected mutagenesis of the Trypanosoma cruzi trans-sialidase enzyme identifies two domains involved in its sialyltransferase activity.
[6]
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.
[7]
PubMed ID14580216
JournalBiochemistry
Year2003
Volume42
Pages12682-90
AuthorsWatson JN, Dookhun V, Borgford TJ, Bennet AJ
TitleMutagenesis of the conserved active-site tyrosine changes a retaining sialidase into an inverting sialidase.
[8]
CommentsX-ray crystallography
PubMed ID15527797
JournalFEBS Lett
Year2004
Volume577
Pages265-9
AuthorsWatson JN, Newstead S, Dookhun V, Taylor G, Bennet AJ
TitleContribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from Micromonospora viridifaciens.
Related PDB1w8n,1w8o
[9]
PubMed ID15966735
JournalBiochemistry
Year2005
Volume44
Pages9117-22
AuthorsNewstead S, Watson JN, Knoll TL, Bennet AJ, Taylor G
TitleStructure and mechanism of action of an inverting mutant sialidase.
Related PDB2ber

comments
This enzyme belongs to the glycosidase family-33. This enzyme is composed of three domains, the N-terminal catalytic domain, Immunoglobulin-like domain, and the C-terminal F5/8 type C domain.
Although Sodium is included as a cofactor, it is not involved in catalysis. It maintains the conformation of the C-terminal domain.(see [3])
According to the literature [7], the catalytic reaction proceeds as follows:
(1) Asp92 acts as a general acid, to protonate the leaving group, through a water molecule, to give an oxacarbenium ion-like transition state. (SN1-like reaction)
(2) Tyr370, whose pKa is probably modulated by Glu260, makes a nucleophilic attack on the C2 atom of the transition-state, to form a siaryl-enzyme intermediate.
(3) Asp92 acts as a general base, to activate the water.
(4) The activated water makes a nucleophilic attack on the intermediate, to complete the hydrolysis.
###
According to the literature [7], sialyl-based ketal must be much more reactive than ordinary O-glycoside bond.

createdupdated
2005-04-152009-02-26
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 2010)
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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.