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PDBsum entry 1vdd

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protein ligands metals Protein-protein interface(s) links
Recombination PDB id
1vdd
Jmol
Contents
Protein chains
199 a.a. *
Ligands
IMD ×5
Metals
_ZN ×4
Waters ×65
* Residue conservation analysis
PDB id:
1vdd
Name: Recombination
Title: Crystal structure of recombinational repair protein recr
Structure: Recombination protein recr. Chain: a, b, c, d. Fragment: residues 1-199. Engineered: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Gene: recr. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.50Å     R-factor:   0.233     R-free:   0.301
Authors: B.I.Lee,K.H.Kim,S.W.Suh
Key ref:
B.I.Lee et al. (2004). Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair. EMBO J, 23, 2029-2038. PubMed id: 15116069 DOI: 10.1038/sj.emboj.7600222
Date:
20-Mar-04     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZNA2  (RECR_DEIRA) -  Recombination protein RecR
Seq:
Struc:
220 a.a.
199 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1038/sj.emboj.7600222 EMBO J 23:2029-2038 (2004)
PubMed id: 15116069  
 
 
Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.
B.I.Lee, K.H.Kim, S.J.Park, S.H.Eom, H.K.Song, S.W.Suh.
 
  ABSTRACT  
 
RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes. The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix-hairpin-helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30-35 angstroms diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Detailed views of domains/motifs in DR RecR. (A) HhH motifs from two monomers are swapped. Gly21, Arg23 and Lys27 are shown. Primed residues belong to the second subunit B in Figure 2C. (B) Cys[4] zinc-finger motif. (C) Toprim domain with residues Glu86, Asp90 and Glu146. Corresponding positions (142 and 144) of the 'DxD' sequence are indicated by red balls. (D) The C-terminal regions from two monomers are swapped. Arg167 and Asp182 are the fingerprint residues of the canonical Walker B motif. Double-primed residues belong to the third subunit C. The orientations of domains/motifs are roughly similar to those in subunits B (colored in white green), D (purple) and C (white blue) in Figure 2C.
Figure 5.
Figure 5 A possible DNA clamp model for RecR. (A) Comparison of DR RecR with DNA clamp proteins. Ribbon diagrams and electrostatic potential at the molecular surface are shown for DR RecR, E. coli DNA polymerase III subunit, T4 gp45 and human PCNA. The diameter of the central hole is about 30 -35 for DR RecR and about 35 for other clamp proteins. The molecular surface was colored according to the electrostatic potential: blue, 10 kT; white, 0 kT; red, -10 kT. (B) Conserved residues of DR RecR located in the putative DNA-binding region of the central hole (left). Strictly conserved residues are colored in green and semiconserved residues in yellow, as deduced by aligning 14 RecR sequences in Figure 1. Negatively charged residues of the Toprim domain and the Walker B motif that may play a role in Mg2+-enhanced DNA binding (right). (C) Model for dsDNA binding by DR RecR.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2029-2038) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525646 R.M.Leal, G.P.Bourenkov, O.Svensson, D.Spruce, M.Guijarro, and A.N.Popov (2011).
Experimental procedure for the characterization of radiation damage in macromolecular crystals.
  J Synchrotron Radiat, 18, 381-386.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20371513 H.Xu, H.T.Beernink, and S.W.Morrical (2010).
DNA-binding properties of T4 UvsY recombination mediator protein: polynucleotide wrapping promotes high-affinity binding to single-stranded DNA.
  Nucleic Acids Res, 38, 4821-4833.  
19634988 M.A.Wouters, S.W.Fan, and N.L.Haworth (2010).
Disulfides as redox switches: from molecular mechanisms to functional significance.
  Antioxid Redox Signal, 12, 53-91.  
18986990 A.Sakai, and M.M.Cox (2009).
RecFOR and RecOR as Distinct RecA Loading Pathways.
  J Biol Chem, 284, 3264-3272.  
19609302 B.Ren, J.Kühn, L.Meslet-Cladiere, J.Briffotaux, C.Norais, R.Lavigne, D.Flament, R.Ladenstein, and H.Myllykallio (2009).
Structure and function of a novel endonuclease acting on branched DNA substrates.
  EMBO J, 28, 2479-2489.
PDB code: 2vld
19003992 C.Y.Yang, K.H.Chin, M.T.Yang, A.H.Wang, and S.H.Chou (2009).
Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris.
  Proteins, 74, 530-537.
PDB code: 3dfg
19017635 N.Makharashvili, T.Mi, O.Koroleva, and S.Korolev (2009).
RecR-mediated Modulation of RecF Dimer Specificity for Single- and Double-stranded DNA.
  J Biol Chem, 284, 1425-1434.  
18599486 C.Manfredi, B.Carrasco, S.Ayora, and J.C.Alonso (2008).
Bacillus subtilis RecO Nucleates RecA onto SsbA-coated Single-stranded DNA.
  J Biol Chem, 283, 24837-24847.  
18223077 G.Xu, L.Wang, H.Chen, H.Lu, N.Ying, B.Tian, and Y.Hua (2008).
RecO is essential for DNA damage repair in Deinococcus radiodurans.
  J Bacteriol, 190, 2624-2628.  
19116657 J.E.Long, N.Renzette, R.C.Centore, and S.J.Sandler (2008).
Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12.
  PLoS ONE, 3, e4100.  
18000001 J.Inoue, M.Honda, S.Ikawa, T.Shibata, and T.Mikawa (2008).
The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins.
  Nucleic Acids Res, 36, 94.  
18658243 M.Honda, T.Fujisawa, T.Shibata, and T.Mikawa (2008).
RecR forms a ring-like tetramer that encircles dsDNA by forming a complex with RecF.
  Nucleic Acids Res, 36, 5013-5020.  
18937104 R.D.Shereda, A.G.Kozlov, T.M.Lohman, M.M.Cox, and J.L.Keck (2008).
SSB as an organizer/mobilizer of genome maintenance complexes.
  Crit Rev Biochem Mol Biol, 43, 289-318.  
17524514 H.D.Han, A.Lee, T.Hwang, C.K.Song, H.Seong, J.Hyun, and B.C.Shin (2007).
Enhanced circulation time and antitumor activity of doxorubicin by comblike polymer-incorporated liposomes.
  J Control Release, 120, 161-168.  
17581636 J.Timmins, I.Leiros, and S.McSweeney (2007).
Crystal structure and mutational study of RecOR provide insight into its mode of DNA binding.
  EMBO J, 26, 3260-3271.
PDB code: 2v1c
17426134 J.Y.Ha, H.K.Kim, d.o. .J.Kim, K.H.Kim, S.J.Oh, H.H.Lee, H.J.Yoon, H.K.Song, and S.W.Suh (2007).
The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding.
  Nucleic Acids Res, 35, 2671-2681.
PDB code: 2owy
17272275 M.D.Hobbs, A.Sakai, and M.M.Cox (2007).
SSB protein limits RecOR binding onto single-stranded DNA.
  J Biol Chem, 282, 11058-11067.  
17255941 O.Koroleva, N.Makharashvili, C.T.Courcelle, J.Courcelle, and S.Korolev (2007).
Structural conservation of RecF and Rad50: implications for DNA recognition and RecF function.
  EMBO J, 26, 867-877.
PDB code: 2o5v
16675461 M.Honda, J.Inoue, M.Yoshimasu, Y.Ito, T.Shibata, and T.Mikawa (2006).
Identification of the RecR Toprim domain as the binding site for both RecF and RecO. A role of RecR in RecFOR assembly at double-stranded DNA-single-stranded DNA junctions.
  J Biol Chem, 281, 18549-18559.  
16531400 M.P.Killoran, and J.L.Keck (2006).
Three HRDC domains differentially modulate Deinococcus radiodurans RecQ DNA helicase biochemical activity.
  J Biol Chem, 281, 12849-12857.  
16710300 V.Martín, C.Chahwan, H.Gao, V.Blais, J.Wohlschlegel, J.R.Yates, C.H.McGowan, and P.Russell (2006).
Sws1 is a conserved regulator of homologous recombination in eukaryotic cells.
  EMBO J, 25, 2564-2574.  
16132081 E.P.Rocha, E.Cornet, and B.Michel (2005).
Comparative and evolutionary analysis of the bacterial homologous recombination systems.
  PLoS Genet, 1, e15.  
16077031 F.Allemand, N.Mathy, D.Brechemier-Baey, and C.Condon (2005).
The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member.
  Nucleic Acids Res, 33, 4368-4376.  
15719017 I.Leiros, J.Timmins, D.R.Hall, and S.McSweeney (2005).
Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans.
  EMBO J, 24, 906-918.
PDB code: 1w3s
16076958 K.L.Maxwell, P.Reed, R.G.Zhang, S.Beasley, A.R.Walmsley, F.A.Curtis, A.Joachimiak, A.M.Edwards, and G.J.Sharples (2005).
Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange.
  Proc Natl Acad Sci U S A, 102, 11260-11265.
PDB code: 1pc6
16151089 Q.Banh, M.Arenskötter, and A.Steinbüchel (2005).
Establishment of Tn5096-based transposon mutagenesis in Gordonia polyisoprenivorans.
  Appl Environ Microbiol, 71, 5077-5084.  
16301798 Z.Q.Fu (2005).
Three-dimensional model-free experimental error correction of protein crystal diffraction data with free-R test.
  Acta Crystallogr D Biol Crystallogr, 61, 1643-1648.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.