EzCatDB: T00065
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DB codeT00065
RLCP classification1.31.36210.99 : Hydrolysis
CATH domainDomain 12.120.10.10 : NeuraminidaseCatalytic domain
Domain 22.60.40.10 : Immunoglobulin-like
Domain 32.60.120.260 : Jelly Rolls
E.C.3.2.1.18
CSA1euu

CATH domainRelated DB codes (homologues)
2.120.10.10 : NeuraminidaseD00173,M00310,T00064,T00208
2.60.120.260 : Jelly RollsM00124,T00005,T00066
2.60.40.10 : Immunoglobulin-likeM00131,T00257,T00005,M00113,M00127,M00132,M00323,M00325,M00327,M00329,M00330,M00331,M00332,T00307,D00166,D00500,M00112,M00193,T00063,T00067,T00245

Enzyme Name
UniProtKBKEGG

Q02834
Protein nameSialidaseexo-alpha-sialidase
neuraminidase
sialidase
alpha-neuraminidase
acetylneuraminidase
SynonymsEC 3.2.1.18
Neuraminidase
PfamPF00754 (F5_F8_type_C)
PF10633 (NPCBM_assoc)
[Graphical view]
CAZyGH33 (Glycoside Hydrolase Family)

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

UniProtKB: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

Compound table: links to PDB-related databases & PoSSuM

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
ChEBI29101






15377
17012







PubChem923






962
22247451
439197







                        
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 UniProtKBQ02834
[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 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 - )
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