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PDBsum entry 1t4g

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protein ligands metals links
Recombination PDB id
1t4g
Jmol
Contents
Protein chain
299 a.a. *
Ligands
ANP
Metals
_MG ×2
Waters ×121
* Residue conservation analysis
PDB id:
1t4g
Name: Recombination
Title: Atpase in complex with amp-pnp
Structure: DNA repair and recombination protein rada. Chain: a. Engineered: yes. Mutation: yes
Source: Methanococcus voltae. Organism_taxid: 2188. Gene: rada. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.219     R-free:   0.244
Authors: Y.Wu,Y.He,I.A.Moya,X.Qian,Y.Luo
Key ref:
Y.Wu et al. (2004). Crystal structure of archaeal recombinase RADA: a snapshot of its extended conformation. Mol Cell, 15, 423-435. PubMed id: 15304222 DOI: 10.1016/j.molcel.2004.07.014
Date:
29-Apr-04     Release date:   17-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O73948  (RADA_METVO) -  DNA repair and recombination protein RadA
Seq:
Struc:
322 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1016/j.molcel.2004.07.014 Mol Cell 15:423-435 (2004)
PubMed id: 15304222  
 
 
Crystal structure of archaeal recombinase RADA: a snapshot of its extended conformation.
Y.Wu, Y.He, I.A.Moya, X.Qian, Y.Luo.
 
  ABSTRACT  
 
Homologous recombination of DNA plays crucial roles in repairing severe DNA damage and in generating genetic diversity. The process is facilitated by a superfamily of recombinases: bacterial RecA, archaeal RadA and Rad51, and eukaryal Rad51 and DMC1. These recombinases share a common ATP-dependent filamentous quaternary structure for binding DNA and facilitating strand exchange. We have determined the crystal structure of Methanococcus voltae RadA in complex with the ATP analog AMP-PNP at 2.0 A resolution. The RadA filament is a 106.7 A pitch helix with six subunits per turn. The DNA binding loops L1 and L2 are located in close proximity to the filament axis. The ATP analog is buried between two RadA subunits, a feature similar to that of the active filament of Escherichia coli RecA revealed by electron microscopy. The disposition of the N-terminal domain suggests a role of the Helix-hairpin-Helix motif in binding double-stranded DNA.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. ATP-Mediated Subunit Interface
Figure 4.
Figure 4. Structural Comparison of RadA and Rad51 Recombinases
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 15, 423-435) copyright 2004.  
  Figures were selected by the author.  
 
 
    Author's comment    
 
  In agreement with features of active filaments of E. coli RecA orthologue reconstructed by electron microscopy, this crystal structure of archaeal RadA / Rad51 from methanococcus voltae revealed an ATP-bridged file of protomers at atomic resolution. Expectedly, the equivalent loops to RecA's DNA-binding L1 and L2 are located along the filament axis where DNA strand exchange is believed to take place.
Yu Luo
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20062530 A.L.Okorokov, Y.L.Chaban, D.V.Bugreev, J.Hodgkinson, A.V.Mazin, and E.V.Orlova (2010).
Structure of the hDmc1-ssDNA filament reveals the principles of its architecture.
  PLoS One, 5, e8586.  
20441441 M.Patel, Q.Jiang, R.Woodgate, M.M.Cox, and M.F.Goodman (2010).
A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V.
  Crit Rev Biochem Mol Biol, 45, 171-184.  
20015079 W.Kagawa, and H.Kurumizaka (2010).
From meiosis to postmeiotic events: uncovering the molecular roles of the meiosis-specific recombinase Dmc1.
  FEBS J, 277, 590-598.  
19066203 A.A.Grigorescu, J.H.Vissers, D.Ristic, Y.Z.Pigli, T.W.Lynch, C.Wyman, and P.A.Rice (2009).
Inter-subunit interactions that coordinate Rad51's activities.
  Nucleic Acids Res, 37, 557-567.  
19540850 D.Lucarelli, Y.A.Wang, V.E.Galkin, X.Yu, D.B.Wigley, and E.H.Egelman (2009).
The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.
  J Mol Biol, 391, 269-274.  
19076215 J.Hikiba, Y.Takizawa, S.Ikawa, T.Shibata, and H.Kurumizaka (2009).
Biochemical analysis of the human DMC1-I37N polymorphism.
  FEBS J, 276, 457-465.  
19327367 R.B.Robertson, D.N.Moses, Y.Kwon, P.Chan, W.Zhao, P.Chi, H.Klein, P.Sung, and E.C.Greene (2009).
Visualizing the disassembly of S. cerevisiae Rad51 nucleoprotein filaments.
  J Mol Biol, 388, 703-720.  
19465774 Y.Li, Y.He, and Y.Luo (2009).
Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis.
  Acta Crystallogr D Biol Crystallogr, 65, 602-610.
PDB codes: 3etl 3ew9 3ewa
19447914 Y.Morozumi, Y.Takizawa, M.Takaku, and H.Kurumizaka (2009).
Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities.
  Nucleic Acids Res, 37, 4296-4307.  
19295907 Y.W.Chang, T.P.Ko, C.D.Lee, Y.C.Chang, K.A.Lin, C.S.Chang, A.H.Wang, and T.F.Wang (2009).
Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity.
  PLoS ONE, 4, e4890.
PDB codes: 2zub 2zuc 2zud
19102758 A.I.Roca, A.E.Almada, and A.C.Abajian (2008).
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.
  BMC Bioinformatics, 9, 554.  
18385131 D.M.Baitin, M.C.Gruenig, and M.M.Cox (2008).
SSB antagonizes RecX-RecA interaction.
  J Biol Chem, 283, 14198-14204.  
18566005 J.Hikiba, K.Hirota, W.Kagawa, S.Ikawa, T.Kinebuchi, I.Sakane, Y.Takizawa, S.Yokoyama, B.Mandon-Pépin, A.Nicolas, T.Shibata, K.Ohta, and H.Kurumizaka (2008).
Structural and functional analyses of the DMC1-M200V polymorphism found in the human population.
  Nucleic Acids Res, 36, 4181-4190.
PDB code: 2zjb
18603529 J.M.Cox, H.Li, E.A.Wood, S.Chitteni-Pattu, R.B.Inman, and M.M.Cox (2008).
Defective Dissociation of a "Slow" RecA Mutant Protein Imparts an Escherichia coli Growth Defect.
  J Biol Chem, 283, 24909-24921.  
19020353 J.R.Prabu, G.P.Manjunath, N.R.Chandra, K.Muniyappa, and M.Vijayan (2008).
Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes.
  Acta Crystallogr D Biol Crystallogr, 64, 1146-1157.
PDB codes: 2zr0 2zr7 2zr9 2zra 2zrb 2zrc 2zrd 2zre 2zrf 2zrg 2zrh 2zri 2zrj 2zrk 2zrl 2zrm 2zrn 2zro 2zrp
18927106 P.S.Malik, and L.S.Symington (2008).
Rad51 gain-of-function mutants that exhibit high affinity DNA binding cause DNA damage sensitivity in the absence of Srs2.
  Nucleic Acids Res, 36, 6504-6510.  
18173750 T.Ishida, Y.Takizawa, I.Sakane, and H.Kurumizaka (2008).
The Lys313 residue of the human Rad51 protein negatively regulates the strand-exchange activity.
  Genes Cells, 13, 91.  
18497818 Z.Chen, H.Yang, and N.P.Pavletich (2008).
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
  Nature, 453, 489-484.
PDB codes: 3cmt 3cmu 3cmv 3cmw 3cmx
17302439 A.L.Forget, M.S.Loftus, D.A.McGrew, B.T.Bennett, and K.L.Knight (2007).
The human Rad51 K133A mutant is functional for DNA double-strand break repair in human cells.
  Biochemistry, 46, 3566-3575.  
17329376 L.T.Chen, T.P.Ko, Y.C.Chang, K.A.Lin, C.S.Chang, A.H.Wang, and T.F.Wang (2007).
Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins.
  Nucleic Acids Res, 35, 1787-1801.
PDB code: 2dfl
17848989 L.T.Chen, T.P.Ko, Y.W.Chang, K.A.Lin, A.H.Wang, and T.F.Wang (2007).
Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein.
  PLoS ONE, 2, e858.
PDB code: 2z43
17483448 M.I.Petalcorin, V.E.Galkin, X.Yu, E.H.Egelman, and S.J.Boulton (2007).
Stabilization of RAD-51-DNA filaments via an interaction domain in Caenorhabditis elegans BRCA2.
  Proc Natl Acad Sci U S A, 104, 8299-8304.  
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
17502105 M.Modesti, D.Ristic, T.van der Heijden, C.Dekker, J.van Mameren, E.J.Peterman, G.J.Wuite, R.Kanaar, and C.Wyman (2007).
Fluorescent human RAD51 reveals multiple nucleation sites and filament segments tightly associated along a single DNA molecule.
  Structure, 15, 599-609.  
17515903 O.R.Davies, and L.Pellegrini (2007).
Interaction with the BRCA2 C terminus protects RAD51-DNA filaments from disassembly by BRC repeats.
  Nat Struct Mol Biol, 14, 475-483.  
16717288 C.Wiese, J.M.Hinz, R.S.Tebbs, P.B.Nham, S.S.Urbin, D.W.Collins, L.H.Thompson, and D.Schild (2006).
Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination.
  Nucleic Acids Res, 34, 2833-2843.  
16895466 C.Wyman, and R.Kanaar (2006).
DNA double-strand break repair: all's well that ends well.
  Annu Rev Genet, 40, 363-383.  
16765886 C.Wyman (2006).
Monomer networking activates recombinases.
  Structure, 14, 949-950.  
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
17098184 E.H.Egelman (2006).
RecA assembly, one molecule at a time.
  Structure, 14, 1600-1602.  
16527806 J.M.Cox, S.N.Abbott, S.Chitteni-Pattu, R.B.Inman, and M.M.Cox (2006).
Complementation of one RecA protein point mutation by another. Evidence for trans catalysis of ATP hydrolysis.
  J Biol Chem, 281, 12968-12975.  
16914443 M.K.Shivji, O.R.Davies, J.M.Savill, D.L.Bates, L.Pellegrini, and A.R.Venkitaraman (2006).
A region of human BRCA2 containing multiple BRC repeats promotes RAD51-mediated strand exchange.
  Nucleic Acids Res, 34, 4000-4011.  
16382157 M.Kojic, Q.Zhou, M.Lisby, and W.K.Holloman (2006).
Rec2 interplay with both Brh2 and Rad51 balances recombinational repair in Ustilago maydis.
  Mol Cell Biol, 26, 678-688.  
16945962 N.Sarai, W.Kagawa, T.Kinebuchi, A.Kagawa, K.Tanaka, K.Miyagawa, S.Ikawa, T.Shibata, H.Kurumizaka, and S.Yokoyama (2006).
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein.
  Nucleic Acids Res, 34, 4429-4437.  
16648362 R.Krishna, G.P.Manjunath, P.Kumar, A.Surolia, N.R.Chandra, K.Muniyappa, and M.Vijayan (2006).
Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.
  Nucleic Acids Res, 34, 2186-2195.
PDB code: 2g88
16684994 R.Rajan, J.W.Wisler, and C.E.Bell (2006).
Probing the DNA sequence specificity of Escherichia coli RECA protein.
  Nucleic Acids Res, 34, 2463-2471.  
16765891 V.E.Galkin, Y.Wu, X.P.Zhang, X.Qian, Y.He, X.Yu, W.D.Heyer, Y.Luo, and E.H.Egelman (2006).
The Rad51/RadA N-terminal domain activates nucleoprotein filament ATPase activity.
  Structure, 14, 983-992.
PDB code: 2gdj
17050545 X.Qian, Y.He, X.Ma, M.N.Fodje, P.Grochulski, and Y.Luo (2006).
Calcium stiffens archaeal Rad51 recombinase from Methanococcus voltae for homologous recombination.
  J Biol Chem, 281, 39380-39387.
PDB code: 2i1q
16780572 Y.Matsuo, I.Sakane, Y.Takizawa, M.Takahashi, and H.Kurumizaka (2006).
Roles of the human Rad51 L1 and L2 loops in DNA binding.
  FEBS J, 273, 3148-3159.  
15755748 A.Ariza, D.J.Richard, M.F.White, and C.S.Bond (2005).
Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA.
  Nucleic Acids Res, 33, 1465-1473.
PDB code: 2bke
16194225 C.E.Bell (2005).
Structure and mechanism of Escherichia coli RecA ATPase.
  Mol Microbiol, 58, 358-366.  
15944450 D.Ristic, M.Modesti, T.van der Heijden, J.van Noort, C.Dekker, R.Kanaar, and C.Wyman (2005).
Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function.
  Nucleic Acids Res, 33, 3292-3302.  
15917244 D.V.Bugreev, E.I.Golub, A.Z.Stasiak, A.Stasiak, and A.V.Mazin (2005).
Activation of human meiosis-specific recombinase Dmc1 by Ca2+.
  J Biol Chem, 280, 26886-26895.  
15642265 E.Skordalakes, A.P.Brogan, B.S.Park, H.Kohn, and J.M.Berger (2005).
Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.
  Structure, 13, 99.
PDB codes: 1xpo 1xpr 1xpu
15956102 T.Akiba, N.Ishii, N.Rashid, M.Morikawa, T.Imanaka, and K.Harata (2005).
Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly.
  Nucleic Acids Res, 33, 3412-3423.
PDB codes: 2cvf 2cvh
15917243 T.Kinebuchi, W.Kagawa, H.Kurumizaka, and S.Yokoyama (2005).
Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding.
  J Biol Chem, 280, 28382-28387.  
15937124 V.E.Galkin, F.Esashi, X.Yu, S.Yang, S.C.West, and E.H.Egelman (2005).
BRCA2 BRC motifs bind RAD51-DNA filaments.
  Proc Natl Acad Sci U S A, 102, 8537-8542.  
15908697 X.P.Zhang, K.I.Lee, J.A.Solinger, K.Kiianitsa, and W.D.Heyer (2005).
Gly-103 in the N-terminal domain of Saccharomyces cerevisiae Rad51 protein is critical for DNA binding.
  J Biol Chem, 280, 26303-26311.  
15537659 Y.Wu, X.Qian, Y.He, I.A.Moya, and Y.Luo (2005).
Crystal structure of an ATPase-active form of Rad51 homolog from Methanococcus voltae. Insights into potassium dependence.
  J Biol Chem, 280, 722-728.
PDB code: 1xu4
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 codes are shown on the right.