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PDBsum entry 2w0m

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protein ligands metals links
Unknown function PDB id
2w0m
Jmol
Contents
Protein chain
220 a.a. *
Ligands
POP
Metals
_ZN ×4
Waters ×98
* Residue conservation analysis
PDB id:
2w0m
Name: Unknown function
Title: Crystal structure of sso2452 from sulfolobus solfataricus p2
Structure: Sso2452. Chain: a. Fragment: residues 1-235. Engineered: yes
Source: Sulfolobus solfataricus p2. Organism_taxid: 273057. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: bl21.
Resolution:
2.00Å     R-factor:   0.202     R-free:   0.250
Authors: A.Mcrobbie,L.Carter,K.A.Johnson,M.Kerou,H.Liu,S.Mcmahon,M.Ok J.H.Naismith,M.F.White
Key ref:
A.M.McRobbie et al. (2009). Structural and Functional Characterisation of a Conserved Archaeal RadA Paralog with Antirecombinase Activity. J Mol Biol, 389, 661-673. PubMed id: 19414020 DOI: 10.1016/j.jmb.2009.04.060
Date:
19-Aug-08     Release date:   19-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q97VZ8  (Q97VZ8_SULSO) -  Uncharacterized protein
Seq:
Struc:
262 a.a.
220 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA metabolic process   2 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
DOI no: 10.1016/j.jmb.2009.04.060 J Mol Biol 389:661-673 (2009)
PubMed id: 19414020  
 
 
Structural and Functional Characterisation of a Conserved Archaeal RadA Paralog with Antirecombinase Activity.
A.M.McRobbie, L.G.Carter, M.Kerou, H.Liu, S.A.McMahon, K.A.Johnson, M.Oke, J.H.Naismith, M.F.White.
 
  ABSTRACT  
 
DNA recombinases (RecA in bacteria, Rad51 in eukarya and RadA in archaea) catalyse strand-exchange between homologous DNA molecules, the central reaction of homologous recombination, and are among the most conserved DNA repair proteins known. In bacteria, RecA is the sole protein responsible for this reaction, whereas, in eukaryotes, there are several RAD51 paralogs that cooperate to catalyse strand exchange. All archaea have at least one (and as many as four) RadA paralogs, but their function remains unclear. Here we show the three RadA paralogs encoded by the Sulfolobus solfataricus genome are expressed under normal growth conditions, and are not UV-inducible. We demonstrate that one of these proteins, Sso2452, which is representative of the large aRadC sub-family of archaeal RadA paralogs, functions as an ATPase that binds tightly to ssDNA. However, Sso2452 is not an active recombinase in vitro, and inhibits D-loop formation by RadA. We present the high-resolution crystal structure of Sso2452, which reveals key structural differences from the canonical RecA family recombinases that may explain its functional properties. The possible roles of the archaeal RadA paralogs in vivo are discussed.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Strand-exchange activity of Sso2452 and RadA. (a) Schematic of the strand-exchange assay and substrate design. Length (nucleotides) of oligonucleotide is indicated above the strand. Black circles denote the ^32P radiolabel. (b) Sso2452 (4 μM) or RadA (4 μM) was preincubated with ^32P-radiolabelled ssDNA (50mer) for 3 min prior to addition of dsDNA (25mer) and incubation for up to 10 min at 60 °C. Both show strand-exchange activity. (c) Order of addition experiments. Protein 1 was preincubated with ssDNA for 3 min prior to the addition of the second protein. Following a further 3-min incubation, dsDNA was added to initiate the reaction. (d) Strand-exchange reactions with Alba1 (10 μM) and SSB (10 μM). Reactions were performed as described above. Alba1 supports strand-exchange activity, but SSB does not. For all panels, time points shown are 0.5, 1, 3, 5, 8 and 10 min. Controls used were as follows: c1, DNA species in the absence of protein after 10 min at 60 °C; c2, size marker for the strand-exchange product; and c3, reactions lacking ATP/MgCl[2] after 10 min.
Figure 5.
Fig. 5. Structural biology of SSo2452. (a) A ribbon representation of the monomer of SSo2452 shown in slate blue. The four Zn^2+ ions that are believed to be an artifact of crystallisation are shown as gray spheres. The termini of the disordered L2 DNA binding loop from residues Q166 to G178 are shown as yellow spheres. The pyrophosphate modelled into the electron density is shown as spheres. (b) Superposition of Sso2452 (shown as slate blue wire) with the hexameric Pho0284 (shown as wire; colored differently for each monomer, with the superimposing monomer shown in red). In Pho0284, ADP (shown in space filling) binds at the interface of the hexamer. Two of the Zn^2+ ions in our crystal (shown as gray spheres) disrupt this crystal packing arrangement and thus ATP binding. The PPi molecule shown in (a) overlaps with the phosphates of the ADP molecule in Pho0284. (c) Structural superposition of the S. solfataricus RadA (yellow ribbon; PDB code 2bke) and Sso2452 (colored as above). RadA has an extra NTD implicated in multimerisation and dsDNA binding, linked to the core domain by a short polymerisation motif (PM) that includes a conserved phenylalanine residue (F73) that acts as the “ball” in the “ball-and-socket” joint formed in RadA filaments. The ATPase domain that consists of a central β-sheet and flanking α-helices is common to both structures. (d) Sequence comparison for the L1 and L2 ssDNA binding loops in RadA and aRadC. Residues in bold are discussed in the text.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 389, 661-673) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22948927 S.S.Cha, Y.J.An, C.S.Jeong, M.K.Kim, S.G.Lee, K.H.Lee, and B.H.Oh (2012).
Experimental phasing using zinc anomalous scattering.
  Acta Crystallogr D Biol Crystallogr, 68, 1253-1258.
PDB codes: 4dt3 4dwz 4fc5
21265740 M.F.White (2011).
Homologous recombination in the archaea: the means justify the ends.
  Biochem Soc Trans, 39, 15-19.  
20371520 J.Chen, N.Villanueva, M.A.Rould, and S.W.Morrical (2010).
Insights into the mechanism of Rad51 recombinase from the structure and properties of a filament interface mutant.
  Nucleic Acids Res, 38, 4889-4906.
PDB code: 3lda
20419351 M.Oke, L.G.Carter, K.A.Johnson, H.Liu, S.A.McMahon, X.Yan, M.Kerou, N.D.Weikart, N.Kadi, M.A.Sheikh, S.Schmelz, M.Dorward, M.Zawadzki, C.Cozens, H.Falconer, H.Powers, I.M.Overton, C.A.van Niekerk, X.Peng, P.Patel, R.A.Garrett, D.Prangishvili, C.H.Botting, P.J.Coote, D.T.Dryden, G.J.Barton, U.Schwarz-Linek, G.L.Challis, G.L.Taylor, M.F.White, and J.H.Naismith (2010).
The Scottish Structural Proteomics Facility: targets, methods and outputs.
  J Struct Funct Genomics, 11, 167-180.
PDB codes: 2ivy 2jg5 2jg6 2vw8 2vxz 2wj9 2x0o 2x3d 2x3e 2x3f 2x3g 2x3l 2x3m 2x3n 2x3o 2x48 2x4g 2x4h 2x4i 2x4j 2x4k 2x4l 2x5c 2x5d 2x5e 2x5f 2x5g 2x5h 2x5p 2x5q 2x5r 2x5t 2x7b 2x7i 2xu2
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.