PDBsum entry 2fn9

Sugar binding protein

PDB id: 2fn9

Contents

Protein chains

280 a.a. *

Waters ×627

* Residue conservation analysis

PDB id:

2fn9

Name:

Sugar binding protein

Title:

Thermotoga maritima ribose binding protein unliganded form

Structure:

Ribose abc transporter, periplasmic ribose-binding protein. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm0958. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.181 R-free: 0.203

Authors:

M.J.Cuneo,A.Changela,Y.Tian,L.S.Beese,H.W.Hellinga

Key ref:

M.J.Cuneo et al. (2008). Ligand-induced conformational changes in a thermophilic ribose-binding protein. Bmc Struct Biol, 8, 50-50. PubMed id: 19019243

Date:

10-Jan-06 Release date: 16-Jan-07

Protein chains

Q9X053  (Q9X053_THEMA) -  Ribose ABC transporter, periplasmic ribose-binding protein from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 323 a.a.

Struc: 280 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

Bmc Struct Biol 8:50-50 (2008)

PubMed id: 19019243

Ligand-induced conformational changes in a thermophilic ribose-binding protein.

M.J.Cuneo, L.S.Beese, H.W.Hellinga.

ABSTRACT

BACKGROUND: Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. RESULTS: Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (app Tm value is 108 degrees C) than the mesophilic Escherichia coli homolog (ecRBP) (app Tm value is 56 degrees C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. CONCLUSION: Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.