spacer
spacer

PDBsum entry 3beq

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
3beq
Jmol
Contents
Protein chains
385 a.a.
Ligands
NAG
GOL ×10
ACT ×5
PO4
NAG-NAG-MAN-MAN
Metals
_CA ×5
Waters ×756
PDB id:
3beq
Name: Hydrolase
Title: Neuraminidase of a/brevig mission/1/1918 h1n1 strain
Structure: Neuraminidase. Chain: a, b. Fragment: residues 83-467. Engineered: yes
Source: Influenza a virus. Organism_taxid: 11320. Strain: a/brevig mission/1/1918. Gene: na. Expressed in: trichoplusia ni. Expression_system_taxid: 7111.
Resolution:
1.64Å     R-factor:   0.182     R-free:   0.210
Authors: X.Xu,X.Zhu,I.A.Wilson
Key ref: X.Xu et al. (2008). Structural characterization of the 1918 influenza virus H1N1 neuraminidase. J Virol, 82, 10493-10501. PubMed id: 18715929
Date:
19-Nov-07     Release date:   30-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9IGQ6  (NRAM_I18A0) -  Neuraminidase
Seq:
Struc:
469 a.a.
385 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.18  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     exo-alpha-sialidase activity     1 term  

 

 
J Virol 82:10493-10501 (2008)
PubMed id: 18715929  
 
 
Structural characterization of the 1918 influenza virus H1N1 neuraminidase.
X.Xu, X.Zhu, R.A.Dwek, J.Stevens, I.A.Wilson.
 
  ABSTRACT  
 
Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 "Spanish flu" (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-A and 1.45-A resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147 to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20978010 D.C.Watson, S.Leclerc, W.W.Wakarchuk, and N.M.Young (2011).
Enzymatic synthesis and properties of glycoconjugates with legionaminic acid as a replacement for neuraminic acid.
  Glycobiology, 21, 99.  
21211019 J.Abdussamad, and S.Aris-Brosou (2011).
The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host.
  BMC Evol Biol, 11, 6.  
21426903 L.C.Tsai, C.H.Hsiao, W.Y.Liu, L.M.Yin, and L.F.Shyur (2011).
Structural basis for the inhibition of 1,3-1,4-β-D-glucanase by noncompetitive calcium ion and competitive Tris inhibitors.
  Biochem Biophys Res Commun, 407, 593-598.  
20981560 M.Sarkar, A.S.Agrawal, R.Sharma Dey, S.Chattopadhyay, R.Mullick, P.De, S.Chakrabarti, and M.Chawla-Sarkar (2011).
Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India.
  Arch Virol, 156, 207-217.  
21326879 P.M.Schmidt, R.M.Attwood, P.G.Mohr, S.A.Barrett, and J.L.McKimm-Breschkin (2011).
A generic system for the expression and purification of soluble and stable influenza neuraminidase.
  PLoS One, 6, e16284.  
21206954 Y.Li, H.Cao, H.Yu, Y.Chen, K.Lau, J.Qu, V.Thon, G.Sugiarto, and X.Chen (2011).
Identifying selective inhibitors against the human cytosolic sialidase NEU2 by substrate specificity studies.
  Mol Biosyst, 7, 1060-1072.  
20427241 J.D.Durrant, and J.A.McCammon (2010).
Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design.
  Comput Biol Chem, 34, 97.  
20845954 J.D.Durrant, and J.A.McCammon (2010).
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes.
  J Chem Inf Model, 50, 1865-1871.  
21209916 J.Wu, F.Zhang, M.Wang, C.Xu, J.Song, J.Zhou, X.Lin, Y.Zhang, X.Wu, W.Tan, J.Lu, H.Zhao, J.Gao, P.Zhao, J.Lu, and Y.Wang (2010).
Characterization of neuraminidases from the highly pathogenic avian H5N1 and 2009 pandemic H1N1 influenza A viruses.
  PLoS One, 5, e15825.  
20852645 Q.Li, J.Qi, W.Zhang, C.J.Vavricka, Y.Shi, J.Wei, E.Feng, J.Shen, J.Chen, D.Liu, J.He, J.Yan, H.Liu, H.Jiang, M.Teng, X.Li, and G.F.Gao (2010).
The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site.
  Nat Struct Mol Biol, 17, 1266-1268.
PDB code: 3nss
  20029608 D.Parks, N.Macdonald, and R.Beiko (2009).
Tracking the evolution and geographic spread of Influenza A.
  PLoS Curr, 1, RRN1014.  
  20029609 L.Le, E.Lee, K.Schulten, and T.N.Truong (2009).
Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza.
  PLoS Curr, 1, RRN1015.  
  20198180 M.Danishuddin, S.N.Khan, and A.U.Khan (2009).
Phylogenetic analysis of surface proteins of novel H1N1 virus isolated from 2009 pandemic.
  Bioinformation, 4, 94-97.  
  20025203 N.Macdonald, D.Parks, and R.Beiko (2009).
SeqMonitor: influenza analysis pipeline and visualization.
  PLoS Curr, 1, RRN1040.  
19457254 S.Maurer-Stroh, J.Ma, R.T.Lee, F.L.Sirota, and F.Eisenhaber (2009).
Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites.
  Biol Direct, 4, 18; discussion 18.  
19927983 T.Naito, A.Kawaguchi, and K.Nagata (2009).
[Function of influenza virus RNA polymerase based on structure]
  Uirusu, 59, 1.  
19580433 V.M.Deyde, and L.V.Gubareva (2009).
Influenza genome analysis using pyrosequencing method: current applications for a moving target.
  Expert Rev Mol Diagn, 9, 493-509.  
19124660 V.M.Deyde, T.Nguyen, R.A.Bright, A.Balish, B.Shu, S.Lindstrom, A.I.Klimov, and L.V.Gubareva (2009).
Detection of molecular markers of antiviral resistance in influenza A (H5N1) viruses using a pyrosequencing method.
  Antimicrob Agents Chemother, 53, 1039-1047.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.