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Hydrolase PDB id
1d2m
Jmol
Contents
Protein chain
552 a.a. *
Ligands
BOG ×3
SO4
Waters ×335
* Residue conservation analysis
PDB id:
1d2m
Name: Hydrolase
Title: Uvrb protein of thermus thermophilus hb8; a nucleotide excis enzyme
Structure: Excinuclease abc subunit b. Chain: a. Synonym: uvrb. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.234     R-free:   0.253
Authors: N.Nakagawa,M.Sugahara,R.Masui,R.Kato,K.Fukuyama,S.Kuramitsu, Structural Genomics/proteomics Initiative (Rsgi)
Key ref: N.Nakagawa et al. (1999). Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair. J Biochem (tokyo), 126, 986-990. PubMed id: 10578047
Date:
25-Sep-99     Release date:   22-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q56243  (UVRB_THET8) -  UvrABC system protein B
Seq:
Struc: 		 
Seq:
Struc: 		665 a.a.
552 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
J Biochem (tokyo) 126:986-990 (1999)
PubMed id: 10578047  
 
 
Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair.
N.Nakagawa, M.Sugahara, R.Masui, R.Kato, K.Fukuyama, S.Kuramitsu.
 
  ABSTRACT  
 
In the nucleotide excision repair system, UvrB plays a central role in damage recognition and DNA incision by interacting with UvrA and UvrC. We have determined the crystal structure of Thermus thermophilus HB8 UvrB at 1.9 A resolution. UvrB comprises four domains, two of which have an alpha/beta structure resembling the core domains of DNA and RNA helicases. Additionally, UvrB has an alpha-helical domain and a domain consisting of antiparallel beta-sheets (beta-domain). The sequence similarity suggests that the beta-domain interacts with UvrA. Based on the distribution of the conserved regions and the structure of the PcrA-DNA complex, a model for the UvrB-DNA complex is proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
21054499 Y.Agari, S.Kuramitsu, and A.Shinkai (2010).
Identification of novel genes regulated by the oxidative stress-responsive transcriptional activator SdrP in Thermus thermophilus HB8.
  FEMS Microbiol Lett, 313, 127-134.  
18248777 D.L.Croteau, M.J.DellaVecchia, L.Perera, and B.Van Houten (2008).
Cooperative damage recognition by UvrA and UvrB: identification of UvrA residues that mediate DNA binding.
  DNA Repair (Amst), 7, 392-404.  
18158267 D.Pakotiprapha, Y.Inuzuka, B.R.Bowman, G.F.Moolenaar, N.Goosen, D.Jeruzalmi, and G.L.Verdine (2008).
Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding.
  Mol Cell, 29, 122-133.
PDB code: 2r6f
16532007 J.J.Truglio, E.Karakas, B.Rhau, H.Wang, M.J.DellaVecchia, B.Van Houten, and C.Kisker (2006).
Structural basis for DNA recognition and processing by UvrB.
  Nat Struct Mol Biol, 13, 360-364.
PDB code: 2fdc
16935877 M.P.Killoran, and J.L.Keck (2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
  Nucleic Acids Res, 34, 4098-4105.  
15718299 S.Rocak, B.Emery, N.K.Tanner, and P.Linder (2005).
Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs.
  Nucleic Acids Res, 33, 999.  
16051821 T.Xu, A.Sampath, A.Chao, D.Wen, M.Nanao, P.Chene, S.G.Vasudevan, and J.Lescar (2005).
Structure of the Dengue virus helicase/nucleoside triphosphatase catalytic domain at a resolution of 2.4 A.
  J Virol, 79, 10278-10288.
PDB codes: 2bhr 2bmf
15065864 H.Ma, and Y.Zou (2004).
Thermodynamic characterization of the interaction of mutant UvrB protein with damaged DNA.
  Biochemistry, 43, 4206-4211.  
15585580 H.Shi, O.Cordin, C.M.Minder, P.Linder, and R.M.Xu (2004).
Crystal structure of the human ATP-dependent splicing and export factor UAP56.
  Proc Natl Acad Sci U S A, 101, 17628-17633.
PDB codes: 1xti 1xtj 1xtk
15192705 J.J.Truglio, D.L.Croteau, M.Skorvaga, M.J.DellaVecchia, K.Theis, B.S.Mandavilli, B.Van Houten, and C.Kisker (2004).
Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair.
  EMBO J, 23, 2498-2509.
PDB code: 1t5l
15247343 M.Kampmann, and D.Stock (2004).
Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling.
  Nucleic Acids Res, 32, 3537-3545.  
15065863 Y.Zou, H.Ma, I.G.Minko, S.M.Shell, Z.Yang, Y.Qu, Y.Xu, N.E.Geacintov, and R.S.Lloyd (2004).
DNA damage recognition of mutated forms of UvrB proteins in nucleotide excision repair.
  Biochemistry, 43, 4196-4205.  
14580212 Y.Zou, S.M.Shell, C.D.Utzat, C.Luo, Z.Yang, N.E.Geacintov, and A.K.Basu (2003).
Effects of DNA adduct structure and sequence context on strand opening of repair intermediates and incision by UvrABC nuclease.
  Biochemistry, 42, 12654-12661.  
11823434 A.C.Rodríguez, and D.Stock (2002).
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
  EMBO J, 21, 418-426.
PDB codes: 1gku 1gl9
12145219 E.E.Verhoeven, C.Wyman, G.F.Moolenaar, and N.Goosen (2002).
The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands.
  EMBO J, 21, 4196-4205.  
11842222 I.G.Minko, Y.Zou, and R.S.Lloyd (2002).
Incision of DNA-protein crosslinks by UvrABC nuclease suggests a potential repair pathway involving nucleotide excision repair.
  Proc Natl Acad Sci U S A, 99, 1905-1909.  
11839499 J.M.Caruthers, and D.B.McKay (2002).
Helicase structure and mechanism.
  Curr Opin Struct Biol, 12, 123-133.  
11713311 A.Yamagata, R.Masui, Y.Kakuta, S.Kuramitsu, and K.Fukuyama (2001).
Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain.
  Nucleic Acids Res, 29, 4617-4624.  
11157766 E.E.Verhoeven, C.Wyman, G.F.Moolenaar, J.H.Hoeijmakers, and N.Goosen (2001).
Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition.
  EMBO J, 20, 601-611.  
11689453 G.F.Moolenaar, L.Höglund, and N.Goosen (2001).
Clue to damage recognition by UvrB: residues in the beta-hairpin structure prevent binding to non-damaged DNA.
  EMBO J, 20, 6140-6149.  
11459984 X.Yu, S.A.Jacobs, S.C.West, T.Ogawa, and E.H.Egelman (2001).
Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA.
  Proc Natl Acad Sci U S A, 98, 8419-8424.  
11087862 J.M.Caruthers, E.R.Johnson, and D.B.McKay (2000).
Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase.
  Proc Natl Acad Sci U S A, 97, 13080-13085.
PDB codes: 1fuk 1fuu
  11206052 Y.Kuroda, K.Tani, Y.Matsuo, and S.Yokoyama (2000).
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics.
  Protein Sci, 9, 2313-2321.  
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 code is shown on the right.