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PDBsum entry 2r6f

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2r6f
Jmol
Contents
Protein chains
899 a.a. *
Ligands
ADP ×4
Metals
_ZN ×6
Waters ×4
* Residue conservation analysis
PDB id:
2r6f
Name: Hydrolase
Title: Crystal structure of bacillus stearothermophilus uvra
Structure: Excinuclease abc subunit a. Chain: a, b. Fragment: uvra. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 272567. Strain: 10. Gene: uvra. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
3.20Å     R-factor:   0.257     R-free:   0.292
Authors: Y.Inuzuka,D.Pakotiprapha,B.R.Bowman,D.Jeruzalmi,G.L.Verdine
Key ref:
D.Pakotiprapha et al. (2008). Crystal Structure of Bacillus stearothermophilus UvrA Provides Insight into ATP-Modulated Dimerization, UvrB Interaction, and DNA Binding. Mol Cell, 29, 122-133. PubMed id: 18158267 DOI: 10.1016/j.molcel.2007.10.026
Date:
05-Sep-07     Release date:   08-Jan-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5KVB6  (Q5KVB6_GEOKA) -  UvrABC system protein A
Seq:
Struc:
 
Seq:
Struc:
955 a.a.
899 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     excinuclease repair complex   2 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   7 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
DOI no: 10.1016/j.molcel.2007.10.026 Mol Cell 29:122-133 (2008)
PubMed id: 18158267  
 
 
Crystal Structure of Bacillus stearothermophilus UvrA Provides Insight into ATP-Modulated Dimerization, UvrB Interaction, and DNA Binding.
D.Pakotiprapha, Y.Inuzuka, B.R.Bowman, G.F.Moolenaar, N.Goosen, D.Jeruzalmi, G.L.Verdine.
 
  ABSTRACT  
 
The nucleotide excision repair pathway corrects many structurally unrelated DNA lesions. Damage recognition in bacteria is performed by UvrA, a member of the ABC ATPase superfamily whose functional form is a dimer with four nucleotide-binding domains (NBDs), two per protomer. In the 3.2 A structure of UvrA from Bacillus stearothermophilus, we observe that the nucleotide-binding sites are formed in an intramolecular fashion and are not at the dimer interface as is typically found in other ABC ATPases. UvrA also harbors two unique domains; we show that one of these is required for interaction with UvrB, its partner in lesion recognition. In addition, UvrA contains three zinc modules, the number and ligand sphere of which differ from previously published models. Structural analysis, biochemical experiments, surface electrostatics, and sequence conservation form the basis for models of ATP-modulated dimerization, UvrA-UvrB interaction, and DNA binding during the search for lesions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structural Comparison of the NBDs of BstUvrA and Other ABC ATPases
The conserved ATPase motifs are colored as follows: Walker A/P loop, green; Walker B and D loop, orange; ABC signature motif, blue; Q loop, magenta; and H loop/switch, cyan.
(A) Arrangement of the NBDs in E. coli MalK, Pyrococcus furiosus RLI, and BstUvrA. Key residues important for nucleotide binding and interactions across the dimer interface are shown. The transmembrane portion of MalK is depicted in transparent yellow.
(B) NBDs of UvrA were superimposed with the NBDs of the maltose transporter MalK (ADP-bound, PDB code 2AWO; ATP-bound, PDB code 1Q12), and Rad50 (ATP-bound, PDB code 1F2U) using their respective ATP-binding domains. All the motifs are from the same NBD except for the ABC signature motif and the D loop, which are part of the opposing NBD. The bound ADP is from the proximal site of UvrA protomer A and is represented as ball and stick.
(C) Histogram showing the distance between the C[α] atoms of the conserved Lys residue in the Walker A motif and Ser residue in the ABC signature motif in the structures of ABC ATPases solved in the dimeric state (PDB codes 2R6F, 2AWO, 1Q1B, 1Q1E, 2AWN, 1YQT, 1L7V, 2ONK, 1Q12, 1F2U, 1XEF, 1XEX).
Figure 4.
Figure 4. BstUvrA Dimer Interface
C[α] trace of protomers A and B are shown in pale green and pale blue, respectively, with the Zn atoms in gray. The regions involved in polar contacts across the dimer interface are shown using ribbon diagram (green and orange, protomer A; blue and magenta, protomer B). Hydrogen bonds are depicted as dashed lines and the bound ADP molecules as space-filling models. Illustrations in (A) –(C) are shown in the same orientation as in Figure 1B.
(A) UvrA dimer.
(B) Interactions between the Q loop-I and the loop following α helix 1, which contains the Walker A-I motif at its N terminus.
(C) Interactions between the loop preceding Walker B-I and residues of the ATP-binding domain I of the opposing monomer.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2008, 29, 122-133) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22307053 D.Pakotiprapha, M.Samuels, K.Shen, J.H.Hu, and D.Jeruzalmi (2012).
Structure and mechanism of the UvrA-UvrB DNA damage sensor.
  Nat Struct Mol Biol, 19, 291-298.
PDB codes: 3uwx 3ux8
21393072 K.Wagner, G.F.Moolenaar, and N.Goosen (2011).
Role of the insertion domain and the zinc-finger motif of Escherichia coli UvrA in damage recognition and ATP hydrolysis.
  DNA Repair (Amst), 10, 483-496.  
21240268 M.Jaciuk, E.Nowak, K.Skowronek, A.Tańska, and M.Nowotny (2011).
Structure of UvrA nucleotide excision repair protein in complex with modified DNA.
  Nat Struct Mol Biol, 18, 191-197.
PDB code: 3pih
20502938 J.L.Tubbs, and J.A.Tainer (2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
  Cell Mol Life Sci, 67, 3749-3762.  
21145481 L.Manelyte, Y.I.Kim, A.J.Smith, R.M.Smith, and N.J.Savery (2010).
Regulation and rate enhancement during transcription-coupled DNA repair.
  Mol Cell, 40, 714-724.  
20572869 M.Kivisaar (2010).
Mechanisms of stationary-phase mutagenesis in bacteria: mutational processes in pseudomonads.
  FEMS Microbiol Lett, 312, 1.  
20227373 N.M.Kad, H.Wang, G.G.Kennedy, D.M.Warshaw, and B.Van Houten (2010).
Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single- molecule imaging of quantum-dot-labeled proteins.
  Mol Cell, 37, 702-713.  
  20981145 R.Morita, S.Nakane, A.Shimada, M.Inoue, H.Iino, T.Wakamatsu, K.Fukui, N.Nakagawa, R.Masui, and S.Kuramitsu (2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
  J Nucleic Acids, 2010, 179594.  
19287003 D.Pakotiprapha, Y.Liu, G.L.Verdine, and D.Jeruzalmi (2009).
A Structural Model for the Damage-sensing Complex in Bacterial Nucleotide Excision Repair.
  J Biol Chem, 284, 12837-12844.
PDB code: 3fpn
19549864 H.Wang, M.Lu, M.S.Tang, B.Van Houten, J.B.Ross, M.Weinfeld, and X.C.Le (2009).
DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway.
  Proc Natl Acad Sci U S A, 106, 12849-12854.  
19368888 J.Timmins, E.Gordon, S.Caria, G.Leonard, S.Acajjaoui, M.S.Kuo, V.Monchois, and S.McSweeney (2009).
Structural and mutational analyses of Deinococcus radiodurans UvrA2 provide insight into DNA binding and damage recognition by UvrAs.
  Structure, 17, 547-558.
PDB codes: 2vf7 2vf8
19208636 K.Wagner, G.Moolenaar, J.van Noort, and N.Goosen (2009).
Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer.
  Nucleic Acids Res, 37, 1962-1972.  
19700770 M.N.Murphy, P.Gong, K.Ralto, L.Manelyte, N.J.Savery, and K.Theis (2009).
An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd.
  Nucleic Acids Res, 37, 6042-6053.
PDB code: 3hjh
19183285 M.Pruteanu, and T.A.Baker (2009).
Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage.
  Mol Microbiol, 71, 912-924.  
19474351 M.Samuels, G.Gulati, J.H.Shin, R.Opara, E.McSweeney, M.Sekedat, S.Long, Z.Kelman, and D.Jeruzalmi (2009).
A biochemically active MCM-like helicase in Bacillus cereus.
  Nucleic Acids Res, 37, 4441-4452.  
19748784 P.M.Jones, M.L.O'Mara, and A.M.George (2009).
ABC transporters: a riddle wrapped in a mystery inside an enigma.
  Trends Biochem Sci, 34, 520-531.  
19544044 V.Kos, and R.C.Ford (2009).
The ATP-binding cassette family: a structural perspective.
  Cell Mol Life Sci, 66, 3111-3126.  
18535149 A.L.Davidson, E.Dassa, C.Orelle, and J.Chen (2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
  Microbiol Mol Biol Rev, 72, 317.  
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
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.