PDBsum entry 1ogc

Transport

PDB id: 1ogc

Contents

Protein chains

131 a.a. *

Metals

_CL ×2

Waters ×186

* Residue conservation analysis

PDB id:

1ogc

Name:

Transport

Title:

The structure of bacillus subtilis rbsd complexed with d-ribose

Structure:

High affinity ribose transport protein rbsd. Chain: a, b, c, d, e. Synonym: cytoplasmic ribose-binding protein rbsd

Source:

Bacillus subtilis. Organism_taxid: 1423

Biol. unit:

Decamer (from PDB file)

Resolution:

2.00Å R-factor: 0.202 R-free: 0.231

Authors:

M.-S.Kim,B.-H.Oh

Key ref:

M.S.Kim et al. (2003). Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture. J Biol Chem, 278, 28173-28180. PubMed id: 12738765 DOI: 10.1074/jbc.M304523200

Date:

30-Apr-03 Release date: 01-Sep-03

Protein chains

P36946  (RBSD_BACSU) -  D-ribose pyranase from Bacillus subtilis (strain 168)

Seq: 131 a.a.

Struc: 131 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.99.62 - D-ribose pyranase.
• Reaction: beta-D-ribopyranose = beta-D-ribofuranose

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M304523200

J Biol Chem 278:28173-28180 (2003)

PubMed id: 12738765

Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture.

M.S.Kim, J.Shin, W.Lee, H.S.Lee, B.H.Oh.

ABSTRACT

RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.

Selected figure(s)

Figure 1.
FIG. 1. Structure and ribose-binding site of RbsD. a, decameric assembly of RbsD shown in two different orientations. Ribose molecules bound to the intersubunit clefts are shown as ball-and-sticks. b, ribbon diagram of RbsD monomer. The secondary structures are numbered in the order of appearance in the primary sequence. c, buried ion cage. A negatively charged ion (in cyan), which is putatively a Cl-, is bound between two RbsD subunits related by the molecular 2-fold axis that superimposes the pentameric rings. The symmetry-related pairs are shown in different colors. Water molecules are in red. Two histidine residues hydrogen-bonded to the bound water molecules are shown.

Figure 3.
FIG. 3. Binding of ribose and ribose 5-phosphate to RbsD. a, binding of D-ribose. The -pyranoside form of the sugar is fitted into the final 2F[o] - F[c] map (1.95 Å, 1.1 ). The C-4-OH group interacts with the C-terminal carboxyl group via a water molecule. The density of this water molecule is weak or unobserved in 2 of 5 binding sites. These weak interactions are not shown. b, surface representation of the intersubunit cleft. The bound ribose is displayed in CPK mode with the oxygen and carbon atoms in red and black, respectively. The bound water molecule is in blue. c, binding of D-ribose 5-phosphate. The phosphorylated sugar is in the -furanose form, which was determined at the beginning of the refinement. The final 2F[o] - F[c] map (2.05 Å, 1.1 ) is shown. His-20 from one RbsD subunit is shown in cyan, and rest of the residues from the adjacent subunit are shown in green. Figs. 1 and 3 were prepared with the program Bobscript (26).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 28173-28180) copyright 2003.

Figures were selected by an automated process.