PDBsum entry 2b8h

Hydrolase

PDB id: 2b8h

Contents

Protein chains

388 a.a. *

Ligands

NAG-NAG ×4

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN ×3

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN

NAG ×4

SO4 ×29

GOL ×3

Metals

_CL ×4

Waters ×1373

* Residue conservation analysis

PDB id:

2b8h

Name:

Hydrolase

Title:

A/nws/whale/maine/1/84 (h1n9) reassortant influenza virus neuraminidase

Structure:

Neuraminidase. Chain: a, b, c, d. Fragment: residues 82-469. Engineered: yes

Source:

Influenza a virus. Organism_taxid: 11320. Expressed in: gallus gallus. Expression_system_taxid: 9031. Expression_system_tissue: egg

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å R-factor: 0.141 R-free: 0.189

Authors:

B.J.Smith,D.Platis,M.M.J.Cox,T.Huyton,R.P.Joosten,J.L.Mckimm- Breschkin,J.-G.Zhang,C.S.Luo,M.-Z.Lou,T.P.J.Garrett,N.E.Labrou

Key ref:

B.J.Smith et al. (2006). Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding. Acta Crystallogr D Biol Crystallogr, 62, 947-952. PubMed id: 16929094 DOI: 10.1107/S0907444906020063

Date:

07-Oct-05 Release date: 05-Sep-06

Protein chains

P05803  (NRAM_I84A1) -  Neuraminidase from Influenza A virus (strain A/Whale/Maine/1/1984 H13N9)

Seq: 470 a.a.

Struc: 388 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.18 - exo-alpha-sialidase.
• 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.

DOI no: 10.1107/S0907444906020063

Acta Crystallogr D Biol Crystallogr 62:947-952 (2006)

PubMed id: 16929094

Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding.

B.J.Smith, T.Huyton, R.P.Joosten, J.L.McKimm-Breschkin, J.G.Zhang, C.S.Luo, M.Z.Lou, N.E.Labrou, T.P.Garrett.

ABSTRACT

The X-ray structure of influenza virus neuraminidase (NA) isolated from whale, subtype N9, has been determined at 2.2 A resolution and contains a tetrameric protein in the asymmetric unit. In structures of NA determined previously, a calcium ion is observed to coordinate amino acids near the substrate-binding site. In three of the NA monomers determined here this calcium is absent, resulting in structural alterations near the substrate-binding site. These changes affect the conformation of residues that participate in several key interactions between the enzyme and substrate and provide at a molecular level the basis of the structural and functional role of calcium in substrate and inhibitor binding. Several sulfate ions were identified in complex with the protein. These are located in the active site, occupying the space reserved for the substrate (sialic acid) carboxylate, and in positions leading away from the substrate-binding site. These sites offer a new opportunity for the design of inhibitors of influenza virus NA.

Selected figure(s)

Figure 1.
Figure 1 Ribbon diagram of the calcium-binding site and structural changes between calcium-bound (green, chain A) and calcium-free (cyan, chain B; pink, chain C; tan, chain D) forms of NA. The loops L1 (245-251), L2 (295-298) and L3 (343-344) adopt different conformations in the four monomers. In the calcium-bound form, the protein backbone carbonyl O atoms of Asp293, Gly297 and Asn347 and the side-chain carboxylate of Asp324 all bind the calcium cation (yellow sphere). In the calcium-free form of chain B, the carbonyl groups of Gly297 and Asn347 are shown to be flipped from the conformation observed in the calcium-bound form.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 947-952) copyright 2006.

Figure was selected by the author.

Author's comment

The structure of a crystal form of influenza virus neuraminidase that reveals the absence of a calcium ion in a high-affinity site near the substrate-binding site. Structural changes associated with the absence of this ion explain the requirement of calcium for activity and thermostability of the enzyme. Sulfate ions were observed in and near the active site of this enzyme, and may form the basis of the design of a new class of inhibitor of this enzyme. (Platis, D., Smith, B.J., Huyton, T., Labrou, N.E. Biochem. J. (2006) 399, 215-223).
B.J. SMITH