spacer
spacer

PDBsum entry 3nn9

Go to PDB code: 
protein ligands metals links
Hydrolase(o-glycosyl) PDB id
3nn9
Jmol
Contents
Protein chain
388 a.a. *
Ligands
NAG-NAG-BMA-MAN-
MAN-MAN-MAN
NAG ×2
Metals
_CA
Waters ×89
* Residue conservation analysis
PDB id:
3nn9
Name: Hydrolase(o-glycosyl)
Title: Refined atomic structures of n9 subtype influenza virus neur and escape mutants
Structure: Neuraminidase n9. Chain: a. Engineered: yes
Source: Unidentified influenza virus. Organism_taxid: 11309
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.178    
Authors: W.R.Tulip,J.N.Varghese,A.T.Baker,A.Vandonkelaar,W.G.Laver, R.G.Webster,P.M.Colman
Key ref: W.R.Tulip et al. (1991). Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants. J Mol Biol, 221, 487-497. PubMed id: 1920429
Date:
28-Mar-91     Release date:   15-Jul-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03472  (NRAM_I75A5) -  Neuraminidase
Seq:
Struc:
470 a.a.
388 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 Mol Biol 221:487-497 (1991)
PubMed id: 1920429  
 
 
Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants.
W.R.Tulip, J.N.Varghese, A.T.Baker, A.van Donkelaar, W.G.Laver, R.G.Webster, P.M.Colman.
 
  ABSTRACT  
 
The crystal structure of the N9 subtype neuraminidase of influenza virus was refined by simulated annealing and conventional techniques to an R-factor of 0.172 for data in the resolution range 6.0 to 2.2 A. The r.m.s. deviation from ideal values of bond lengths is 0.014 A. The structure is similar to that of N2 subtype neuraminidase both in secondary structure elements and in their connections. The three-dimensional structures of several escape mutants of neuraminidase, selected with antineuraminidase monoclonal antibodies, are also reported. In every case, structural changes associated with the point mutation are confined to the mutation site or to residues that are spatially immediately adjacent to it. The failure of antisera to cross-react between N2 and N9 subtypes may be correlated with the absence of conserved, contiguous surface structures of area 700 A2 or more.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18849342 N.Wang, E.J.Glidden, S.R.Murphy, B.R.Pearse, and D.N.Hebert (2008).
The Cotranslational Maturation Program for the Type II Membrane Glycoprotein Influenza Neuraminidase.
  J Biol Chem, 283, 33826-33837.  
15608653 K.Stummeyer, A.Dickmanns, M.Mühlenhoff, R.Gerardy-Schahn, and R.Ficner (2005).
Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F.
  Nat Struct Mol Biol, 12, 90-96.
PDB codes: 1v0e 1v0f
15918777 P.M.Colman (2005).
Zanamivir: an influenza virus neuraminidase inhibitor.
  Expert Rev Anti Infect Ther, 3, 191-199.  
11381099 M.J.Jedrzejas (2001).
Pneumococcal virulence factors: structure and function.
  Microbiol Mol Biol Rev, 65, 187.  
11413297 M.T.Murrell, M.Porotto, O.Greengard, N.Poltoratskaia, and A.Moscona (2001).
A single amino acid alteration in the human parainfluenza virus type 3 hemagglutinin-neuraminidase glycoprotein confers resistance to the inhibitory effects of zanamivir on receptor binding and neuraminidase activity.
  J Virol, 75, 6310-6320.  
11298736 Y.Wang, K.Yamaguchi, Y.Shimada, X.Zhao, and T.Miyagi (2001).
Site-directed mutagenesis of human membrane-associated ganglioside sialidase: identification of amino-acid residues contributing to substrate specificity.
  Eur J Biochem, 268, 2201-2208.  
10692451 J.J.Pitt, E.Da Silva, and J.J.Gorman (2000).
Determination of the disulfide bond arrangement of Newcastle disease virus hemagglutinin neuraminidase. Correlation with a beta-sheet propeller structural fold predicted for paramyxoviridae attachment proteins.
  J Biol Chem, 275, 6469-6478.  
  8787876 J.L.McKimm-Breschkin, T.J.Blick, A.Sahasrabudhe, T.Tiong, D.Marshall, G.J.Hart, R.C.Bethell, and C.R.Penn (1996).
Generation and characterization of variants of NWS/G70C influenza virus after in vitro passage in 4-amino-Neu5Ac2en and 4-guanidino-Neu5Ac2en.
  Antimicrob Agents Chemother, 40, 40-46.  
8805520 S.Curry, E.Fry, W.Blakemore, R.Abu-Ghazaleh, T.Jackson, A.King, S.Lea, J.Newman, D.Rowlands, and D.Stuart (1996).
Perturbations in the surface structure of A22 Iraq foot-and-mouth disease virus accompanying coupled changes in host cell specificity and antigenicity.
  Structure, 4, 135-145.
PDB code: 4gh4
8591030 A.Gaskell, S.Crennell, and G.Taylor (1995).
The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
  Structure, 3, 1197-1205.
PDB codes: 1eur 1eus 1eut 1euu
  7549872 J.N.Varghese, V.C.Epa, and P.M.Colman (1995).
Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase.
  Protein Sci, 4, 1081-1087.
PDB codes: 1nnc 7nn9
8592707 M.J.Jedrzejas, S.Singh, W.J.Brouillette, G.M.Air, and M.Luo (1995).
A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase.
  Proteins, 23, 264-277.
PDB code: 1ing
8168505 A.A.Kortt, R.L.Malby, J.B.Caldwell, L.C.Gruen, N.Ivancic, M.C.Lawrence, G.J.Howlett, R.G.Webster, P.J.Hudson, and P.M.Colman (1994).
Recombinant anti-sialidase single-chain variable fragment antibody. Characterization, formation of dimer and higher-molecular-mass multimers and the solution of the crystal structure of the single-chain variable fragment/sialidase complex.
  Eur J Biochem, 221, 151-157.  
  8035509 A.M.Mirza, R.Deng, and R.M.Iorio (1994).
Site-directed mutagenesis of a conserved hexapeptide in the paramyxovirus hemagglutinin-neuraminidase glycoprotein: effects on antigenic structure and function.
  J Virol, 68, 5093-5099.  
  7538848 L.Jin, and J.A.Wells (1994).
Dissecting the energetics of an antibody-antigen interface by alanine shaving and molecular grafting.
  Protein Sci, 3, 2351-2357.  
  7849585 P.M.Colman (1994).
Influenza virus neuraminidase: structure, antibodies, and inhibitors.
  Protein Sci, 3, 1687-1696.  
7994573 R.L.Malby, W.R.Tulip, V.R.Harley, J.L.McKimm-Breschkin, W.G.Laver, R.G.Webster, and P.M.Colman (1994).
The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody.
  Structure, 2, 733-746.
PDB code: 1nmb
  7509002 T.Saito, G.Taylor, W.G.Laver, Y.Kawaoka, and R.G.Webster (1994).
Antigenicity of the N8 influenza A virus neuraminidase: existence of an epitope at the subunit interface of the neuraminidase.
  J Virol, 68, 1790-1796.  
7870741 Y.Suzuki (1994).
Gangliosides as influenza virus receptors. Variation of influenza viruses and their recognition of the receptor sialo-sugar chains.
  Prog Lipid Res, 33, 429-457.  
7680132 J.M.Nuss, P.B.Whitaker, and G.M.Air (1993).
Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza virus neuraminidase.
  Proteins, 15, 121-132.  
8223570 L.C.Gruen, A.A.Kortt, and E.Nice (1993).
Determination of relative binding affinity of influenza virus N9 sialidases with the Fab fragment of monoclonal antibody NC41 using biosensor technology.
  Eur J Biochem, 217, 319-325.  
8397785 L.C.Gruen, T.L.McInerney, R.G.Webster, and D.C.Jackson (1993).
Binding affinity of influenza virus N9 neuraminidase with Fab fragments of monoclonal antibodies NC10 and NC41.
  J Protein Chem, 12, 255-259.  
  8497041 P.M.Colman, P.A.Hoyne, and M.C.Lawrence (1993).
Sequence and structure alignment of paramyxovirus hemagglutinin-neuraminidase with influenza virus neuraminidase.
  J Virol, 67, 2972-2980.  
8452674 R.A.Mariuzza, and R.J.Poljak (1993).
The basics of binding: mechanisms of antigen recognition and mimicry by antibodies.
  Curr Opin Immunol, 5, 50-55.  
8234325 S.J.Crennell, E.F.Garman, W.G.Laver, E.R.Vimr, and G.L.Taylor (1993).
Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase.
  Proc Natl Acad Sci U S A, 90, 9852-9856.
PDB codes: 1sil 1sim
8069621 W.P.Burmeister, B.Henrissat, C.Bosso, S.Cusack, and R.W.Ruigrok (1993).
Influenza B virus neuraminidase can synthesize its own inhibitor.
  Structure, 1, 19-26.
PDB codes: 1nsc 1nsd
1368433 C.Eigenbrot, and A.A.Kossiakoff (1992).
Structural consequences of mutation.
  Curr Opin Biotechnol, 3, 333-337.  
1438172 J.N.Varghese, J.L.McKimm-Breschkin, J.B.Caldwell, A.A.Kortt, and P.M.Colman (1992).
The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor.
  Proteins, 14, 327-332.
PDB code: 2bat
1452222 P.M.Colman (1992).
Structural basis of antigenic variation: studies of influenza virus neuraminidase.
  Immunol Cell Biol, 70, 209-214.  
  1279210 T.Takimoto, W.G.Laver, K.G.Murti, and A.Portner (1992).
Crystallization of biologically active hemagglutinin-neuraminidase glycoprotein dimers proteolytically cleaved from human parainfluenza virus type 1.
  J Virol, 66, 7597-7600.  
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 codes are shown on the right.