PDBsum entry 1ipk

Sugar binding protein

PDB id: 1ipk

Contents

Protein chains

368 a.a. *

* Residue conservation analysis

PDB id:

1ipk

Name:

Sugar binding protein

Title:

Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers

Structure:

Beta-conglycinin, beta chain. Chain: a, b, c. Engineered: yes

Source:

Glycine max. Soybean. Organism_taxid: 3847. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.70Å R-factor: 0.205 R-free: 0.275

Authors:

N.Maruyama,M.Adachi,K.Takahashi,K.Yagasaki,M.Kohno,Y.Takenaka, E.Okuda,S.Nakagawa,B.Mikami,S.Utsumi

Key ref:

N.Maruyama et al. (2001). Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers. Eur J Biochem, 268, 3595-3604. PubMed id: 11422391 DOI: 10.1046/j.1432-1327.2001.02268.x

Date:

16-May-01 Release date: 16-May-02

Protein chains

P25974  (GLCB_SOYBN) -  Beta-conglycinin beta subunit 1 from Glycine max

Seq: 439 a.a.

Struc: 368 a.a.*

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

DOI no: 10.1046/j.1432-1327.2001.02268.x

Eur J Biochem 268:3595-3604 (2001)

PubMed id: 11422391

Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers.

N.Maruyama, M.Adachi, K.Takahashi, K.Yagasaki, M.Kohno, Y.Takenaka, E.Okuda, S.Nakagawa, B.Mikami, S.Utsumi.

ABSTRACT

The crystal structures of recombinant and native beta homotrimers of soybean beta-conglycinin were determined by X-ray crystallography at 2.7 and 2.8 A resolutions, respectively. The crystals of the recombinant and native beta homotrimers belong to space group P21 with cell parameters a = 80.51 A, b = 63.48 A, c = 131.43 A, and beta = 90.01 degrees and with cell parameters a = 82.78 A, b = 69.47 A, c = 125.33 A and beta = 97.22 degrees, respectively. The beta monomers consist of amino-terminal and carboxyl-terminal modules that are very similar to each other and are related by a pseudo-dyad axis. Each module of the beta monomer is subdivided into a core and a loop domain. These structural features of both beta homotrimers are consistent with those of canavalin and phaseolin, which are similar vicilin class proteins. The superposition of the models of the native and recombinant beta monomers shows a root mean square deviation of 0.43-0.51 A for 343 common Calpha atoms within 2.0 A. This result indicates that the N-linked glycans do not influence the final structure of the beta homotrimer. Comparison of the models of beta-conglycinin, phaseolin and canavalin indicates that beta-conglycinin resembles canavalin rather than phaseolin, and that canavalin and phaseolin differ the most among them. The evolutional relationships are discussed.

Selected figure(s)

Figure 1.
Fig. 1. The ribbon diagrams of the recombinant (A and B) and native (C and D) homotrimers. The three monomers in the recombinant and native homotrimers are shown in light blue, light green and pink, and blue, green and magenta, respectively. The carbohydrate moieties of the native homotrimer are shown in yellow as a ball and stick model. The views in (A) and (C) are depicted as threefold symmetry axis runs perpendicular to the paper and the depictions in (B) and (D) are related to the view depicted in (A) and (C) by rotation of 90°. This figure was prepared using MOLSCRIPT and RASTER3D [30,31].

Figure 4.
Fig. 4. The interactions between modules and between monomers in the recombinant , canavalin and phaseolin. Helices and strands are underlined in red and black, respectively. The residues contributing to the hydrophobic interactions and the hydrogen bonds between the modules (A) and between monomers (B) are indicated by magenta letters and yellow shading, respectively. The asterisk shows the conserved salt bridge among the three proteins. The residues which are disordered in at least two monomers are indicated by blue letters. Sequences are aligned with reference to the least-squares fitting by the program TURBOFRODO.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2001, 268, 3595-3604) copyright 2001.

Figures were selected by an automated process.