PDBsum entry 1ba2

Transport

PDB id: 1ba2

Contents

Protein chains

271 a.a. *

Waters ×337

* Residue conservation analysis

PDB id:

1ba2

Name:

Transport

Title:

D67r mutant of d-ribose-binding protein from escherichia coli

Structure:

D-ribose-binding protein. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Cellular_location: periplasmic. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.199 R-free: 0.279

Authors:

A.J.Bjorkman,S.L.Mowbray

Key ref:

A.J.Björkman and S.L.Mowbray (1998). Multiple open forms of ribose-binding protein trace the path of its conformational change. J Mol Biol, 279, 651-664. PubMed id: 9641984 DOI: 10.1006/jmbi.1998.1785

Date:

19-Apr-98 Release date: 15-Jul-98

Protein chains

P02925  (RBSB_ECOLI) -  Ribose import binding protein RbsB from Escherichia coli (strain K12)

Seq: 296 a.a.

Struc: 271 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.1998.1785

J Mol Biol 279:651-664 (1998)

PubMed id: 9641984

Multiple open forms of ribose-binding protein trace the path of its conformational change.

A.J.Björkman, S.L.Mowbray.

ABSTRACT

Conformational changes are necessary for the function of bacterial periplasmic receptors in chemotaxis and transport. Such changes allow entry and exit of ligand, and enable the correct interaction of the ligand-bound proteins with the membrane components of each system. Three open, ligand-free forms of the Escherichia coli ribose-binding protein were observed here by X-ray crystallographic studies. They are opened by 43 degrees, 50 degrees and 64 degrees with respect to the ligand-bound protein reported previously. The three open forms are not distinct, but show a clear relationship to each other. All are the product of a similar opening motion, and are stabilized by a new, almost identical packing interface between the domains. The changes are generated by similar bond rotations, although some differences in the three hinge segments are needed to accommodate the various structural scenarios. Some local repacking also occurs as interdomain contacts are lost. The least open (43 degrees) form is probably the dominant one in solution under normal conditions, although a mixture of species seems likely. The open and closed forms have distinct surfaces in the regions known to be important in chemotaxis and transport, which will differentiate their interactions with the membrane components. It seems certain that the conformational path that links the forms described here is that followed during ligand retrieval, and in ligand release into the membrane-bound permease system.

Selected figure(s)

Figure 3.
Figure 3. The four molecules form a series of related conformations. The closed (green) and mutant A (blue) structures are shown after superposition of domain 1. A single strand of domain 2 (residues 157 to 162) is also shown as a ribbon of the same color for each protein, along with the position of the equivalent strands of the open wt and mutant B structures. The axes of rotation used to bring domain 2 of the closed form onto the same domain of each open molecule are shown, using the colors appropriate to the different open forms. The two views are 90° apart around the visual x-axis.

Figure 5.
Figure 5. The location of sites known to be important in transport (red; residues 11, 12, 45, 52, 67, 72, 165 and 166) and both chemotaxis and transport (blue; residues 44, 70, 73 and 134) are shown for the wild-type closed (a) and open (b) conformations. The residues buried on ligand binding are shown in yellow, and those buried near the hinge in the open forms in cyan. The viewpoint differs from that shown in Figure 4 by approximately 45° around the visual y-axis, and is such that the domains 1 (at bottom) of the two forms are aligned.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 279, 651-664) copyright 1998.

Figures were selected by an automated process.