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Replication PDB id
1c4o
Jmol
Contents
Protein chain
504 a.a. *
Ligands
BOG ×2
SO4 ×4
Waters ×336
* Residue conservation analysis
PDB id:
1c4o
Name: Replication
Title: Crystal structure of the DNA nucleotide excision repair enzy from thermus thermophilus
Structure: DNA nucleotide excision repair enzyme uvrb. Chain: a. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Atcc: 27634. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.252     R-free:   0.266
Authors: M.Machius,L.Henry,M.Palnitkar,J.Deisenhofer
Key ref:
M.Machius et al. (1999). Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. Proc Natl Acad Sci U S A, 96, 11717-11722. PubMed id: 10518516 DOI: 10.1073/pnas.96.21.11717
Date:
14-Sep-99     Release date:   26-Jul-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.
504 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  

 

 
DOI no: 10.1073/pnas.96.21.11717 Proc Natl Acad Sci U S A 96:11717-11722 (1999)
PubMed id: 10518516  
 
 
Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus.
M.Machius, L.Henry, M.Palnitkar, J.Deisenhofer.
 
  ABSTRACT  
 
Nucleotide excision repair (NER) is the most important DNA-repair mechanism in living organisms. In prokaryotes, three enzymes forming the UvrABC system initiate NER of a variety of structurally different DNA lesions. UvrB, the central component of this system, is responsible for the ultimate DNA damage recognition and participates in the incision of the damaged DNA strand. The crystal structure of Thermus thermophilus UvrB reveals a core that is structurally similar to core regions found in helicases, where they constitute molecular motors. Additional domains implicated in binding to DNA and various components of the NER system are attached to this central core. The architecture and distribution of DNA binding sites suggest a possible model for the DNA damage recognition process.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Single isomorphous replacement/anomalous scattering electron density (green) contoured at 2.0 after density modification with the final model superimposed. Shown is the core of helicase domain H2. Carbon atoms are in gray, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow. 		Figure 2.
Fig. 2. (A) Overall topology of Tt UvrB. Domains not visible in the electron density are indicated by blue circles. (B) Functional sites in UvrB. Figs. 1, 2, and 3 were made with BOBSCRIPT (53), GRASP (54), POV-RAY (Persistence of Vision Raytracer, v3.02, POV-Team, www.povray.org), and GL_RENDER (L. Esser, University of Texas Southwestern Medical Center at Dallas).
 
  Figures were selected by an automated process.  

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.  
19762288 L.Manelyte, C.P.Guy, R.M.Smith, M.S.Dillingham, P.McGlynn, and N.J.Savery (2009).
The unstructured C-terminal extension of UvrD interacts with UvrB, but is dispensable for nucleotide excision repair.
  DNA Repair (Amst), 8, 1300-1310.  
19625490 N.T.Uyen, S.Y.Park, J.W.Choi, H.J.Lee, K.Nishi, and J.S.Kim (2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
  Nucleic Acids Res, 37, 6960-6969.
PDB code: 3h1t
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
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
17822711 M.J.DellaVecchia, W.K.Merritt, Y.Peng, T.W.Kirby, E.F.DeRose, G.A.Mueller, B.Van Houten, and R.E.London (2007).
NMR analysis of [methyl-13C]methionine UvrB from Bacillus caldotenax reveals UvrB-domain 4 heterodimer formation in solution.
  J Mol Biol, 373, 282-295.  
17572090 N.J.Savery (2007).
The molecular mechanism of transcription-coupled DNA repair.
  Trends Microbiol, 15, 326-333.  
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
15806108 N.H.Thomä, B.K.Czyzewski, A.A.Alexeev, A.V.Mazin, S.C.Kowalczykowski, and N.P.Pavletich (2005).
Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54.
  Nat Struct Mol Biol, 12, 350-356.
PDB code: 1z3i
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.  
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.  
15256542 P.L.Garcia, G.Bradley, C.J.Hayes, S.Krintel, P.Soultanas, and P.Janscak (2004).
RPA alleviates the inhibitory effect of vinylphosphonate internucleotide linkages on DNA unwinding by BLM and WRN helicases.
  Nucleic Acids Res, 32, 3771-3778.  
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.  
14754162 M.D.Betterton, and F.Jülicher (2003).
A motor that makes its own track: helicase unwinding of DNA.
  Phys Rev Lett, 91, 258103.  
14573947 M.L.Quillin, and B.W.Matthews (2003).
Selling candles in a post-Edison world: phasing with noble gases bound within engineered sites.
  Acta Crystallogr D Biol Crystallogr, 59, 1930-1934.  
12815340 M.Machius (2003).
Structural biology: a high-tech tool for biomedical research.
  Curr Opin Nephrol Hypertens, 12, 431-438.  
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.  
11889086 M.R.Singleton, and D.B.Wigley (2002).
Modularity and specialization in superfamily 1 and 2 helicases.
  J Bacteriol, 184, 1819-1826.  
11173469 A.Cohen, P.Ellis, N.Kresge, and S.M.Soltis (2001).
MAD phasing with krypton.
  Acta Crystallogr D Biol Crystallogr, 57, 233-238.  
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.  
11595187 M.R.Singleton, S.Scaife, and D.B.Wigley (2001).
Structural analysis of DNA replication fork reversal by RecG.
  Cell, 107, 79-89.
PDB code: 1gm5
11452022 R.Soliva, V.Monaco, I.Gómez-Pinto, N.J.Meeuwenoord, G.A.Marel, J.H.Boom, C.González, and M.Orozco (2001).
Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety.
  Nucleic Acids Res, 29, 2973-2985.
PDB codes: 1iek 1iey
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.  
12760078 E.C.Friedberg (2000).
Biological responses to DNA damage: a perspective in the new millennium.
  Cold Spring Harb Symp Quant Biol, 65, 593-602.  
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
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.