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Hydrolase PDB id
2eyq
Jmol
Contents
Protein chains
1146 a.a. *
Ligands
SO4 ×3
EPE ×5
Waters ×120
* Residue conservation analysis
PDB id:
2eyq
Name: Hydrolase
Title: Crystal structure of escherichia coli transcription-repair coupling factor
Structure: Transcription-repair coupling factor. Chain: a, b. Synonym: trcf. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: mfd. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
3.20Å     R-factor:   0.234     R-free:   0.295
Authors: A.M.Deaconescu,S.A.Darst
Key ref:
A.M.Deaconescu et al. (2006). Structural basis for bacterial transcription-coupled DNA repair. Cell, 124, 507-520. PubMed id: 16469698 DOI: 10.1016/j.cell.2005.11.045
Date:
09-Nov-05     Release date:   28-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P30958  (MFD_ECOLI) -  Transcription-repair-coupling factor
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1148 a.a.
1146 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
DOI no: 10.1016/j.cell.2005.11.045 Cell 124:507-520 (2006)
PubMed id: 16469698  
 
 
Structural basis for bacterial transcription-coupled DNA repair.
A.M.Deaconescu, A.L.Chambers, A.J.Smith, B.E.Nickels, A.Hochschild, N.J.Savery, S.A.Darst.
 
  ABSTRACT  
 
Coupling of transcription and DNA repair in bacteria is mediated by transcription-repair coupling factor (TRCF, the product of the mfd gene), which removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair machinery to the site. Here we describe the 3.2 A-resolution X-ray crystal structure of Escherichia coli TRCF. The structure consists of a compact arrangement of eight domains, including a translocation module similar to the SF2 ATPase RecG, and a region of structural similarity to UvrB. Biochemical and genetic experiments establish that another domain with structural similarity to the Tudor-like domain of the transcription elongation factor NusG plays a critical role in TRCF/RNA polymerase interactions. Comparison with the translocation module of RecG as well as other structural features indicate that TRCF function involves large-scale conformational changes. These data, along with a structural model for the interaction of TRCF with the transcription elongation complex, provide mechanistic insights into TRCF function.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Sequence Characteristics of TRCF 		Figure 6.
Figure 6. Structural Model of the TRCF/TEC Assembly
 
  The above figures are reprinted by permission from Cell Press: Cell (2006, 124, 507-520) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21059809 T.Onodera, K.Morino, S.Tokishita, R.Morita, R.Masui, S.Kuramitsu, and T.Ohta (2011).
Role of alkyltransferase-like (ATL) protein in repair of methylated DNA lesions in Thermus thermophilus.
  Mutagenesis, 26, 303-308.  
20606254 D.E.Kainov, V.Cura, M.Vitorino, H.Nierengarten, P.Poussin, B.Kieffer, J.Cavarelli, and A.Poterszman (2010).
Structure determination of the minimal complex between Tfb5 and Tfb2, two subunits of the yeast transcription/DNA-repair factor TFIIH: a retrospective study.
  Acta Crystallogr D Biol Crystallogr, 66, 745-755.  
20371514 D.García-Moreno, J.Abellón-Ruiz, F.García-Heras, F.J.Murillo, S.Padmanabhan, and M.Elías-Arnanz (2010).
CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD.
  Nucleic Acids Res, 38, 4586-4598.  
20716687 J.L.Llácer, J.Espinosa, M.A.Castells, A.Contreras, K.Forchhammer, and V.Rubio (2010).
Structural basis for the regulation of NtcA-dependent transcription by proteins PipX and PII.
  Proc Natl Acad Sci U S A, 107, 15397-15402.
PDB codes: 2xg8 2xgx 2xhk 2xko 2xkp
20702425 L.F.Westblade, E.A.Campbell, C.Pukhrambam, J.C.Padovan, B.E.Nickels, V.Lamour, and S.A.Darst (2010).
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
  Nucleic Acids Res, 38, 8357-8369.
PDB code: 3mlq
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.  
  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.  
20110508 R.T.Pomerantz, and M.O'Donnell (2010).
Direct restart of a replication fork stalled by a head-on RNA polymerase.
  Science, 327, 590-592.  
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19596241 C.L.Stallings, N.C.Stephanou, L.Chu, A.Hochschild, B.E.Nickels, and M.S.Glickman (2009).
CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence.
  Cell, 138, 146-159.  
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
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.  
19747971 M.Pruteanu, and T.A.Baker (2009).
Proteolysis in the SOS response and metal homeostasis in Escherichia coli.
  Res Microbiol, 160, 677-683.  
19458048 M.T.Sung, Y.T.Lai, C.Y.Huang, L.Y.Chou, H.W.Shih, W.C.Cheng, C.H.Wong, and C.Ma (2009).
Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.
  Proc Natl Acad Sci U S A, 106, 8824-8829.
PDB codes: 3fwl 3fwm
19940246 S.R.MacLellan, V.Guariglia-Oropeza, A.Gaballa, and J.D.Helmann (2009).
A two-subunit bacterial sigma-factor activates transcription in Bacillus subtilis.
  Proc Natl Acad Sci U S A, 106, 21323-21328.  
18826409 A.H.Yuan, B.D.Gregory, J.S.Sharp, K.D.McCleary, S.L.Dove, and A.Hochschild (2008).
Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor.
  Mol Microbiol, 70, 1136-1151.  
18166198 D.Nayak, S.Siller, Q.Guo, and R.Sousa (2008).
Mechanism of T7 RNAP pausing and termination at the T7 concatemer junction: a local change in transcription bubble structure drives a large change in transcription complex architecture.
  J Mol Biol, 376, 541-553.  
18786404 G.Shaw, J.Gan, Y.N.Zhou, H.Zhi, P.Subburaman, R.Zhang, A.Joachimiak, D.J.Jin, and X.Ji (2008).
Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.
  Structure, 16, 1417-1427.
PDB code: 3dmq
18729732 J.W.Roberts, S.Shankar, and J.J.Filter (2008).
RNA polymerase elongation factors.
  Annu Rev Microbiol, 62, 211-233.  
18786392 S.Nechaev, and K.Severinov (2008).
RapA: completing the transcription cycle?
  Structure, 16, 1294-1295.  
17329375 A.J.Smith, M.D.Szczelkun, and N.J.Savery (2007).
Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase.
  Nucleic Acids Res, 35, 1802-1811.  
17532270 A.K.Ganesan, A.J.Smith, N.J.Savery, P.Zamos, and P.C.Hanawalt (2007).
Transcription coupled nucleotide excision repair in Escherichia coli can be affected by changing the arginine at position 529 of the beta subunit of RNA polymerase.
  DNA Repair (Amst), 6, 1434-1440.  
17239578 A.M.Deaconescu, N.Savery, and S.A.Darst (2007).
The bacterial transcription repair coupling factor.
  Curr Opin Struct Biol, 17, 96.  
17290000 F.Brueckner, U.Hennecke, T.Carell, and P.Cramer (2007).
CPD damage recognition by transcribing RNA polymerase II.
  Science, 315, 859-862.
PDB codes: 2ja5 2ja6 2ja7 2ja8
17603927 G.Frosina (2007).
The current evidence for defective repair of oxidatively damaged DNA in Cockayne syndrome.
  Free Radic Biol Med, 43, 165-177.  
17896069 J.Wang, P.D.Keightley, and D.L.Halligan (2007).
Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites.
  J Mol Evol, 65, 627-639.  
17506634 M.R.Singleton, M.S.Dillingham, and D.B.Wigley (2007).
Structure and mechanism of helicases and nucleic acid translocases.
  Annu Rev Biochem, 76, 23-50.  
17572090 N.J.Savery (2007).
The molecular mechanism of transcription-coupled DNA repair.
  Trends Microbiol, 15, 326-333.  
16935875 H.Dürr, A.Flaus, T.Owen-Hughes, and K.P.Hopfner (2006).
Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures.
  Nucleic Acids Res, 34, 4160-4167.  
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.