EzCatDB: M00310
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeM00310
CATH domainDomain 1-.-.-.-
Domain 23.30.750.60 : Transcription Regulator spoIIAA
Domain 32.120.10.10 : NeuraminidaseCatalytic domain
Domain 42.40.30.20 : Elongation Factor Tu (Ef-tu); domain 3
Domain 54.10.1090.10 : Endosialidase, domain 4
Domain 6-.-.-.-
Domain 72.-.-.-
Domain 81.-.-.-
E.C.3.2.1.129
CSA1v0e

CATH domainRelated DB codes (homologues)
2.120.10.10 : NeuraminidaseD00173,T00064,T00065,T00208

Enzyme Name
UniProtKBKEGG

Q858B1Q04830
Protein name
Endo-N-acetylneuraminidaseEndo-alpha-sialidase
Endo-N-acylneuraminidase
Endoneuraminidase
Endo-N-acetylneuraminidase
Poly(alpha-2,8-sialosyl) endo-N-acetylneuraminidase
Poly(alpha-2,8-sialoside) alpha-2,8-sialosylhydrolase
Endosialidase
Endo-N
SynonymsEndo-N-acetylneuraminidase
Endo-alpha-sialidase
EC 3.2.1.129
Precursor of gp17
EC 3.2.1.129
Endo-N
EC 3.2.1.129
Endosialidase
G102
RefSeqYP_338127.1 (Protein)
NC_007456.1 (DNA/RNA sequence)

MEROPSS74.001 (Serine)

PfamPF12195 (End_beta_barrel)
PF12217 (End_beta_propel)
PF12218 (End_N_terminal)
PF12219 (End_tail_spike)
PF03906 (Phage_T7_tail)
[Graphical view]
PF12195 (End_beta_barrel)
PF12217 (End_beta_propel)
PF12218 (End_N_terminal)
PF12219 (End_tail_spike)
PF03906 (Phage_T7_tail)
[Graphical view]
CAZyGH58 (Glycoside Hydrolase Family)
GH58 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberQ858B1Q04830
Entry nameQ858B1_BPK1FENAN_BPK1F
ActivityEndohydrolysis of (2->8)-alpha-sialosyl linkages in oligo- or poly(sialic) acids.Endohydrolysis of (2->8)-alpha-sialosyl linkages in oligo- or poly(sialic) acids.
SubunitHomotrimer.Homotrimer.
Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC04466C00001L00073C04466
Compoundalpha-2,8-Linked polymer of sialic acidH2Obeta-sialic acid at reducing end of alpha-2,8-Linked polymer of sialic acidalpha-2,8-Linked polymer of sialic acid
Typeamide group,carboxyl group,polysaccharideH2Oamide group,carboxyl group,polysaccharideamide group,carboxyl group,polysaccharide
ChEBI
15377


PubChem
962
22247451


            
1v0eA01Unbound UnboundUnbound
1v0eB01Unbound UnboundUnbound
1v0eC01Unbound UnboundUnbound
1v0eD01Unbound UnboundUnbound
1v0eE01Unbound UnboundUnbound
1v0eF01Unbound UnboundUnbound
1v0fA01Unbound UnboundUnbound
1v0fB01Unbound UnboundUnbound
1v0fC01Unbound UnboundUnbound
1v0fD01Unbound UnboundUnbound
1v0fE01Unbound UnboundUnbound
1v0fF01Unbound UnboundUnbound
3gvjA01Unbound UnboundUnbound
3gvkA01Unbound UnboundUnbound
3gvkB01Unbound UnboundUnbound
3gvkC01Unbound UnboundUnbound
3gvlA01Unbound UnboundUnbound
3ju4A01Unbound UnboundUnbound
1v0eA02Unbound UnboundUnbound
1v0eB02Unbound UnboundUnbound
1v0eC02Unbound UnboundUnbound
1v0eD02Unbound UnboundUnbound
1v0eE02Unbound UnboundUnbound
1v0eF02Unbound UnboundUnbound
1v0fA02Unbound UnboundUnbound
1v0fB02Unbound UnboundUnbound
1v0fC02Unbound UnboundUnbound
1v0fD02Unbound UnboundUnbound
1v0fE02Unbound UnboundUnbound
1v0fF02Unbound UnboundUnbound
3gvjA02Unbound UnboundUnbound
3gvkA02Unbound Bound:SLB-SIA-SIAUnbound
3gvkB02Unbound Bound:SLB-SIA-SIAUnbound
3gvkC02Unbound Bound:SLB-SIA-SIAUnbound
3gvlA02Unbound UnboundUnbound
3ju4A02Unbound UnboundUnbound
1v0eA03Unbound UnboundUnbound
1v0eB03Unbound UnboundUnbound
1v0eC03Unbound UnboundUnbound
1v0eD03Unbound UnboundUnbound
1v0eE03Unbound UnboundUnbound
1v0eF03Unbound UnboundUnbound
1v0fA03Unbound UnboundUnbound
1v0fB03Unbound UnboundUnbound
1v0fC03Unbound UnboundUnbound
1v0fD03Unbound UnboundUnbound
1v0fE03Unbound UnboundUnbound
1v0fF03Unbound UnboundUnbound
3gvjA03Unbound UnboundUnbound
3gvkA03Unbound UnboundUnbound
3gvkB03Unbound UnboundUnbound
3gvkC03Unbound UnboundUnbound
3gvlA03Unbound UnboundUnbound
3ju4A03Unbound UnboundUnbound
1v0eA04Unbound UnboundUnbound
1v0eB04Unbound UnboundUnbound
1v0eC04Unbound UnboundUnbound
1v0eD04Unbound UnboundUnbound
1v0eE04Unbound UnboundUnbound
1v0eF04Unbound UnboundUnbound
1v0fA04Unbound UnboundUnbound
1v0fB04Unbound UnboundUnbound
1v0fC04Unbound UnboundUnbound
1v0fD04Unbound UnboundUnbound
1v0fE04Unbound UnboundUnbound
1v0fF04Unbound UnboundUnbound
3gvjA04Unbound UnboundUnbound
3gvkA04Unbound UnboundUnbound
3gvkB04Unbound UnboundUnbound
3gvkC04Unbound UnboundUnbound
3gvlA04Unbound UnboundUnbound
3ju4A04Unbound UnboundUnbound
3gw6A01Unbound UnboundUnbound
3gw6B01Unbound UnboundUnbound
3gw6C01Unbound UnboundUnbound
3gw6D01Unbound UnboundUnbound
3gw6E01Unbound UnboundUnbound
3gw6F01Unbound UnboundUnbound
3gw6A02Unbound UnboundUnbound
3gw6B02Unbound UnboundUnbound
3gw6C02Unbound UnboundUnbound
3gw6D02Unbound UnboundUnbound
3gw6E02Unbound UnboundUnbound
3gw6F02Unbound UnboundUnbound
3gw6A03Unbound UnboundUnbound
3gw6B03Unbound UnboundUnbound
3gw6C03Unbound UnboundUnbound
3gw6D03Unbound UnboundUnbound
3gw6E03Unbound UnboundUnbound
3gw6F03Unbound UnboundUnbound
3gw6A04Unbound UnboundUnbound
3gw6B04Unbound UnboundUnbound
3gw6C04Unbound UnboundUnbound
3gw6D04Unbound UnboundUnbound
3gw6E04Unbound UnboundUnbound
3gw6F04Unbound UnboundUnbound

Active-site residues
resource
Literature [6]
pdbCatalytic residuescomment
          
1v0eA01 
 
1v0eB01 
 
1v0eC01 
 
1v0eD01 
 
1v0eE01 
 
1v0eF01 
 
1v0fA01 
 
1v0fB01 
 
1v0fC01 
 
1v0fD01 
 
1v0fE01 
 
1v0fF01 
 
3gvjA01 
 
3gvkA01 
 
3gvkB01 
 
3gvkC01 
 
3gvlA01 
 
3ju4A01 
 
1v0eA02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0eB02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0eC02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0eD02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0eE02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0eF02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0fA02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0fB02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0fC02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0fD02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0fE02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0fF02HIS 350;GLU 581;ARG 596;ARG 647
 
3gvjA02HIS 350;GLU 581;ARG 596;       
mutant R647A
3gvkA02       ;GLU 581;ARG 596;ARG 647
mutant H350A
3gvkB02       ;GLU 581;ARG 596;ARG 647
mutant H350A
3gvkC02       ;GLU 581;ARG 596;ARG 647
mutant H350A
3gvlA02HIS 350;GLU 581;ARG 596;ARG 647
 
3ju4A02HIS 350;GLU 581;ARG 596;ARG 647
 
1v0eA03 
 
1v0eB03 
 
1v0eC03 
 
1v0eD03 
 
1v0eE03 
 
1v0eF03 
 
1v0fA03 
 
1v0fB03 
 
1v0fC03 
 
1v0fD03 
 
1v0fE03 
 
1v0fF03 
 
3gvjA03 
 
3gvkA03 
 
3gvkB03 
 
3gvkC03 
 
3gvlA03 
 
3ju4A03 
 
1v0eA04 
 
1v0eB04 
 
1v0eC04 
 
1v0eD04 
 
1v0eE04 
 
1v0eF04 
 
1v0fA04 
 
1v0fB04 
 
1v0fC04 
 
1v0fD04 
 
1v0fE04 
 
1v0fF04 
 
3gvjA04 
 
3gvkA04 
 
3gvkB04 
 
3gvkC04 
 
3gvlA04 
 
3ju4A04 
 
3gw6A01 
 
3gw6B01 
 
3gw6C01 
 
3gw6D01 
 
3gw6E01 
 
3gw6F01 
 
3gw6A02 
 
3gw6B02 
 
3gw6C02 
 
3gw6D02 
 
3gw6E02 
 
3gw6F02 
 
3gw6A03 
 
3gw6B03 
 
3gw6C03 
 
3gw6D03 
 
3gw6E03 
 
3gw6F03 
 
3gw6A04 
 
3gw6B04 
 
3gw6C04 
 
3gw6D04 
 
3gw6E04 
 
3gw6F04 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]Fig.3, Fig.4, p.347-348

references
[1]
PubMed ID15608653
JournalNat Struct Mol Biol
Year2005
Volume12
Pages90-6
AuthorsStummeyer K, Dickmanns A, Muhlenhoff M, Gerardy-Schahn R, Ficner R
TitleCrystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.
Related PDB1v0e,1v0f
Related UniProtKBQ858B1
[2]
PubMed ID16991177
JournalChembiochem
Year2006
Volume7
Pages1875-7
AuthorsHaselhorst T, Stummeyer K, Muhlenhoff M, Schaper W, Gerardy-Schahn R, von Itzstein M
TitleEndosialidase NF appears to bind polySia DP5 in a helical conformation.
[3]
PubMed ID18558099
JournalCurr Opin Chem Biol
Year2008
Volume12
Pages539-55
AuthorsVocadlo DJ, Davies GJ
TitleMechanistic insights into glycosidase chemistry.
[4]
PubMed ID19411257
JournalJ Biol Chem
Year2009
Volume284
Pages17404-10
AuthorsMorley TJ, Willis LM, Whitfield C, Wakarchuk WW, Withers SG
TitleA new sialidase mechanism: bacteriophage K1F endo-sialidase is an inverting glycosidase.
[5]
PubMed ID20124697
JournalActa Crystallogr D Biol Crystallogr
Year2010
Volume66
Pages176-80
AuthorsSchulz EC, Neumann P, Gerardy-Schahn R, Sheldrick GM, Ficner R
TitleStructure analysis of endosialidase NF at 0.98 A resolution.
Related PDB3ju4
Related UniProtKBQ04830
[6]
PubMed ID20096705
JournalJ Mol Biol
Year2010
Volume397
Pages341-351
AuthorsSchulz EC, Schwarzer D, Frank M, Stummeyer K, Muhlenhoff M, Dickmanns A, Gerardy-Schahn R, Ficner R
TitleStructural Basis for the Recognition and Cleavage of Polysialic Acid by the Bacteriophage K1F Tailspike Protein EndoNF.
Related PDB3gvj,3gvk,3gvl
Related UniProtKBQ858B1

comments
This enzyme belongs to glycosidase family-58, with an inverting mechanism.
According to the literature [6], His350 seems to act as a general acid to protonate the leaving group in the SN1-like reaction. On the other hand, it is not still cleare which group can act as a general base to activate the hydrolytic water, substrate carboxylate or Glu581. Moreover, Arg596 and Arg647 may be involved in catalysis.

createdupdated
2010-04-132012-02-20


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.