PDBsum entry 1i3h

Sugar binding protein

PDB id: 1i3h

Contents

Protein chain

237 a.a. *

Ligands

MAN-MAN

Metals

_CA

_MN

Waters ×253

* Residue conservation analysis

PDB id:

1i3h

Name:

Sugar binding protein

Title:

Concanavalin a-dimannose structure

Structure:

Concanavalin-a. Chain: a. Fragment: residues 164-281,residues 30-148. Synonym: con a,con a

Source:

Canavalia ensiformis. Jack bean. Organism_taxid: 3823

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.20Å R-factor: 0.170 R-free: 0.190

Authors:

D.A.R.Sanders,D.N.Moothoo,J.Raftery,A.J.Howard,J.R.Helliwell, J.H.Naismith

Key ref:

D.A.Sanders et al. (2001). The 1.2 A resolution structure of the Con A-dimannose complex. J Mol Biol, 310, 875-884. PubMed id: 11453694 DOI: 10.1006/jmbi.2001.4806

Date:

15-Feb-01 Release date: 25-Jul-01

Protein chain

P02866  (CONA_CANEN) -  Concanavalin-A from Canavalia ensiformis

Seq: 290 a.a.

Struc: 237 a.a.*

* PDB and UniProt seqs differ at 26 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.2001.4806

J Mol Biol 310:875-884 (2001)

PubMed id: 11453694

The 1.2 A resolution structure of the Con A-dimannose complex.

D.A.Sanders, D.N.Moothoo, J.Raftery, A.J.Howard, J.R.Helliwell, J.H.Naismith.

ABSTRACT

The complex between concanavalin A (Con A) and alpha1-2 mannobiose (mannose alpha1-2 mannose) has been refined to 1.2 A resolution. This is the highest resolution structure reported for any sugar-lectin complex. As the native structure of Con A to 0.94 A resolution is already in the database, this gives us a unique opportunity to examine sugar-protein binding at high resolution. These data have allowed us to model a number of hydrogen atoms involved in the binding of the sugar to Con A, using the difference density map to place the hydrogen atoms. This map reveals the presence of the protonated form of Asp208 involved in binding. Asp208 is not protonated in the 0.94 A native structure. Our results clearly show that this residue is protonated and hydrogen bonds to the sugar. The structure accounts for the higher affinity of the alpha1-2 linked sugar when compared to other disaccharides. This structure identifies different interactions to those predicted by previous modelling studies. We believe that the additional data presented here will enable significant improvements to be made to the sugar-protein modelling algorithms.

Selected figure(s)

Figure 1.
Figure 1. Schematic representation of binding of Man-(a1-2)Man to Con A. Structural water[4] labelled as Wat30. The two conformations for Arg228 (see text and Figure 2) are displayed, with the second conformation designated (Alt). Figure generated using LIGPLOT.[36]

Figure 2.
Figure 2. Stereo view of final 2F[o] - F[c] map showing the alternate conformations adopted by Arg228. The density was modelled at 2 r.m.s. Oxygen atoms are coloured red, nitrogen atoms blue, sulphur atoms yellow and carbon atoms grey. All molecular representations generated using BOBSCRIPT[37] utilizing the GL_RENDER interface (L. Esser & J. Deisenhofer, unpublished data) and POV-Ray(TM).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 875-884) copyright 2001.

Figures were selected by an automated process.