7QSQ | pdb_00007qsq

Permutated N-terminal lobe of the ribose binding protein from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb7QSQ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-14 Released: 2023-01-11
Deposition Author(s): Shanmugaratnam, S., Michel, F., Hocker, B.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structures of permuted halves of a modern ribose-binding protein.

Michel, F., Shanmugaratnam, S., Romero-Romero, S., Hocker, B.

(2023) Acta Crystallogr D Struct Biol 79: 40-49

PubMed: 36601806 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S205979832201186X
Primary Citation Related Structures:
7QSP, 7QSQ

PubMed Abstract:
Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer-dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.

Organizational Affiliation

Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.

Macromolecule Content

Total Structure Weight: 61.88 kDa
Atom Count: 4,446
Modeled Residue Count: 510
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose ABC transporter, periplasmic ribose-binding protein	A, B [auth C], C [auth B], D	138	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_0958
UniProt
Find proteins for Q9X053 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X053 Go to UniProtKB: Q9X053
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X053
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B]	E [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth C], L [auth C], O [auth B], P [auth B], Q [auth D], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]