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PDBsum entry 1u99

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protein ligands links
DNA binding protein PDB id
1u99
Jmol
Contents
Protein chain
301 a.a. *
Ligands
PO4
Waters ×34
* Residue conservation analysis
PDB id:
1u99
Name: DNA binding protein
Title: "Crystal structures of e. Coli reca in a compressed helical filament form 4"
Structure: Reca protein. Chain: a. Synonym: recombinase a. Engineered: yes. Other_details: reca with n-terminal gshm residues
Source: Escherichia coli. Organism_taxid: 562. Gene: reca. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.213     R-free:   0.255
Authors: X.Xing,C.E.Bell
Key ref:
X.Xing and C.E.Bell (2004). Crystal structures of Escherichia coli RecA in a compressed helical filament. J Mol Biol, 342, 1471-1485. PubMed id: 15364575 DOI: 10.1016/j.jmb.2004.07.091
Date:
09-Aug-04     Release date:   21-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7G6  (RECA_ECOLI) -  Protein RecA
Seq:
Struc:
353 a.a.
301 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 stress   9 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
DOI no: 10.1016/j.jmb.2004.07.091 J Mol Biol 342:1471-1485 (2004)
PubMed id: 15364575  
 
 
Crystal structures of Escherichia coli RecA in a compressed helical filament.
X.Xing, C.E.Bell.
 
  ABSTRACT  
 
The X-ray crystal structure of uncomplexed Escherichia coli RecA protein has been determined in three new crystal forms at resolutions of 1.9 A, 2.0 A, and 2.6 A. The RecA protein used for this study contains the extra residues Gly-Ser-His-Met at the N terminus, but retains normal ssDNA-dependent ATPase and coprotease activities. In all three crystals, RecA is packed in a right-handed helical filament with a pitch of approximately 74 A. These RecA filaments are compressed relative to the original crystal structure of RecA, which has a helical pitch of 82.7 A. In the structures of the compressed RecA filament, the monomer-monomer interface and the core domain are essentially the same as in the RecA structure with the 83 A pitch. The change in helical pitch is accommodated by a small movement of the N-terminal domain, which is reoriented to preserve the contacts it makes at the monomer-monomer interface. The new crystal structures show significant variation in the orientation and conformation of the C-terminal domain, as well as in the inter-filament packing interactions. In crystal form 2, a calcium ion is bound closely to a beta-hairpin of the C-terminal domain and to Asp38 of a neighboring filament, and residues 329-331 of the C-terminal tail become ordered to contact a neighboring filament. In crystal forms 3 and 4, a sulfate ion or a phosphate anion is bound to the same site on RecA as the beta-phosphate group of ADP, causing an opening of the P-loop. Altogether, the structures show the conformational variability of RecA protein in the crystalline state, providing insight into many aspects of RecA function.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the RecA monomer from the form 2 crystal. The orientation is the same as for the uppermost monomer (magenta) from the form 2 filament shown in Figure 2c. The a-helices and b-strands of RecA are labeled according to form 1.12 The three calcium ions on the surface are shown as magenta spheres. Residues 66-71 of the P-loop of the ATP-binding site are colored green. Residues 329-331 of the C-terminal tail, which are ordered only in form 2, are shown in blue bonds. The last ordered residues at the ends of loops L1 and L2 are highlighted in orange and red, respectively.
Figure 5.
Figure 5. The N-terminal domain rotates to accommodate compression of the RecA filament. a, Two neighboring monomers in the RecA filament are shown in yellow and cyan in an orientation similar to that of the subunits on the front of the filaments shown in Figure 2. This orientation is chosen to optimize the visibility of the monomer-monomer interaction. Form 1 (PDB code 2REB)12 is shown in continuous lines and form 2 is shown in broken lines. The form 1 and 2 structures are superimposed on the basis of the C^a atoms of the core domains of the monomer on the left. The difference in the helical transformation in forms 1 and 2 is evident from the poor overlap of the monomer on the right. Residues 6 and 33 are labeled to indicate the boundaries of the N-terminal domain. b, Close-up view of a in the region of the monomer-monomer interface. Notice that the orientation of the N-terminal domain of the left monomer is different in the form 1 and form 2 structures, according to the position of the neighboring subunit. The orientation of the N-terminal domain is adjusted to accommodate changes in helical pitch, while preserving atomic interactions at the monomer-monomer interface. This is observed also in the form 3 and form 4 structures, though shown here only for the form 1 and form 2 structures.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 1471-1485) copyright 2004.  
  Figures were selected by an automated process.  

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.  
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.  
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.  
20308162 L.T.Chen, and A.H.Wang (2010).
A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo.
  Nucleic Acids Res, 38, 4361-4371.  
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.  
19027026 J.N.Farb, and S.W.Morrical (2009).
Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.
  J Mol Biol, 385, 393-404.  
19013467 V.E.Galkin, X.Yu, J.Bielnicki, D.Ndjonka, C.E.Bell, and E.H.Egelman (2009).
Cleavage of bacteriophage lambda cI repressor involves the RecA C-terminal domain.
  J Mol Biol, 385, 779-787.  
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
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
17602667 H.Qiu, and Y.Wang (2007).
Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry.
  Anal Chem, 79, 5547-5556.  
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
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
16934834 D.Ndjonka, and C.E.Bell (2006).
Structure of a hyper-cleavable monomeric fragment of phage lambda repressor containing the cleavage site region.
  J Mol Biol, 362, 479-489.
PDB codes: 2hnf 2ho0
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
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
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
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.  
16009134 D.Kidane, and P.L.Graumann (2005).
Intracellular protein and DNA dynamics in competent Bacillus subtilis cells.
  Cell, 122, 73-84.  
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.