3VDP | pdb_00003vdp

Structure and biochemical studies of the recombination mediator protein RecR in RecFOR pathway

PDB DOI: https://doi.org/10.2210/pdb3VDP/pdb

Classification: RECOMBINATION
Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-05 Released: 2012-12-19
Deposition Author(s): Tang, Q., Yan, X.X., Liang, D.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.227 (Depositor), 0.198 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA

Tang, Q., Gao, P., Liu, Y.P., Gao, A., An, X.M., Liu, S., Yan, X.X., Liang, D.C.

(2012) Nucleic Acids Res 40: 11115-11125

PubMed: 23019218 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gks889
Primary Citation Related Structures:
3VDP, 3VDU, 3VE5

PubMed Abstract:
RecR is an important recombination mediator protein in the RecFOR pathway. RecR together with RecO and RecF facilitates RecA nucleoprotein filament formation and homologous pairing. Structural and biochemical studies of Thermoanaerobacter tengcongensis RecR (TTERecR) and its series mutants revealed that TTERecR uses the N-N dimer as a basic functional unit to interact with TTERecO monomer. Two TTERecR N-N dimers form a ring-shaped tetramer via an interaction between their C-terminal regions. The tetramer is a result of crystallization only. Hydrophobic interactions between the entire helix-hairpin-helix domains within the N-terminal regions of two TTERecR monomers are necessary for formation of a RecR functional N-N dimer. The TTERecR N-N dimer conformation also affects formation of a hydrophobic patch, which creates a binding site for TTERecO in the TTERecR Toprim domain. In addition, we demonstrate that TTERecR does not bind single-stranded DNA (ssDNA) and binds double-stranded DNA very weakly, whereas TTERecOR complex can stably bind DNA, with a higher affinity for ssDNA than double-stranded DNA. Based on these results, we propose an interaction model for the RecOR:ssDNA complex.

Organizational Affiliation

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content

Total Structure Weight: 95.22 kDa
Atom Count: 6,481
Modeled Residue Count: 788
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination protein recR	A, B, C, D	212	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 0 Gene Names: recR
UniProt
Find proteins for Q8RDI4 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RDI4 Go to UniProtKB: Q8RDI4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RDI4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] J [auth B] L [auth C] F [auth A], G [auth A], H [auth A], J [auth B], L [auth C], N [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	E [auth A], I [auth B], K [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]