spacer
spacer

PDBsum entry 1ube

Go to PDB code: 
protein ligands links
Recombination PDB id
1ube
Jmol
Contents
Protein chain
303 a.a. *
Ligands
ADP
Waters ×55
* Residue conservation analysis
PDB id:
1ube
Name: Recombination
Title: Msreca-adp complex
Structure: Reca. Chain: a. Synonym: recombinase a. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.30Å     R-factor:   0.221     R-free:   0.290
Authors: S.Datta,R.Krishna,N.Ganesh,N.R.Chandra,K.Muniyappa,M.Vijayan
Key ref: S.Datta et al. (2003). Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes. J Bacteriol, 185, 4280-4284. PubMed id: 12837805
Date:
04-Apr-03     Release date:   22-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q59560  (RECA_MYCS2) -  Protein RecA
Seq:
Struc:
349 a.a.
303 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   6 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
J Bacteriol 185:4280-4284 (2003)
PubMed id: 12837805  
 
 
Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes.
S.Datta, R.Krishna, N.Ganesh, N.R.Chandra, K.Muniyappa, M.Vijayan.
 
  ABSTRACT  
 
The crystal structures of Mycobacterium smegmatis RecA (RecA(Ms)) and its complexes with ADP, ATPgammaS, and dATP show that RecA(Ms) has an expanded binding site like that in Mycobacterium tuberculosis RecA, although there are small differences between the proteins in their modes of nucleotide binding. Nucleotide binding is invariably accompanied by the movement of Gln 196, which appears to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding loops. These observations provide a framework for exploring the known properties of the RecA proteins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21458462 V.E.Galkin, R.L.Britt, L.B.Bane, X.Yu, M.M.Cox, and E.H.Egelman (2011).
Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein.
  J Mol Biol, 408, 815-824.  
20615954 D.F.Warner, D.E.Ndwandwe, G.L.Abrahams, B.D.Kana, E.E.Machowski, C.Venclovas, and V.Mizrahi (2010).
Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis.
  Proc Natl Acad Sci U S A, 107, 13093-13098.  
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
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
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
18453691 P.S.Kaushal, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2008).
Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
  Acta Crystallogr D Biol Crystallogr, 64, 551-560.
PDB code: 2zhx
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
  16880543 J.R.Prabu, S.Thamotharan, J.S.Khanduja, E.Z.Alipio, C.Y.Kim, G.S.Waldo, T.C.Terwilliger, B.Segelke, T.Lekin, D.Toppani, L.W.Hung, M.Yu, E.Bursey, K.Muniyappa, N.R.Chandra, and M.Vijayan (2006).
Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 731-734.
PDB code: 2h5x
16909421 M.Petukhov, D.Lebedev, V.Shalguev, A.Islamov, A.Kuklin, V.Lanzov, and V.Isaev-Ivanov (2006).
Conformational flexibility of RecA protein filament: transitions between compressed and stretched states.
  Proteins, 65, 296-304.  
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
16699190 S.Das, P.Kumar, V.Bhor, A.Surolia, and M.Vijayan (2006).
Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK.
  Acta Crystallogr D Biol Crystallogr, 62, 628-638.
PDB codes: 2ges 2get 2geu 2gev
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
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.  
  16508093 S.Das, P.Kumar, V.Bhor, A.Surolia, and M.Vijayan (2005).
Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 65-67.  
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
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.