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PDBsum entry 1doq

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protein links
Transferase PDB id
1doq
Jmol
Contents
Protein chain
69 a.a. *
* Residue conservation analysis
PDB id:
1doq
Name: Transferase
Title: ThE C-terminal domain of the RNA polymerase alpha subunit from thermus thermophilus
Structure: RNA polymerase alpha subunit. Chain: a. Fragment: c-terminal domain. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: T.Wada,T.Yamazaki,Y.Kyogoku
Key ref:
T.Wada et al. (2000). The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus. J Biol Chem, 275, 16057-16063. PubMed id: 10821859 DOI: 10.1074/jbc.275.21.16057
Date:
21-Dec-99     Release date:   05-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Z9H6  (RPOA_THETH) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
315 a.a.
69 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.275.21.16057 J Biol Chem 275:16057-16063 (2000)
PubMed id: 10821859  
 
 
The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus.
T.Wada, T.Yamazaki, Y.Kyogoku.
 
  ABSTRACT  
 
The C-terminal domain of the alpha subunit of the RNA polymerase (alphaCTD) from Escherichia coli (Ec) regulates transcription by interacting with many kinds of proteins and promoter upstream (UP) elements consisting of AT-rich sequences. However, it is unclear how this system is common in all eubacteria. We investigate the structure and properties of alphaCTD from an extremely thermophilic eubacterium, Thermus thermophilus (Tt). The solution structure of Tt alphaCTD (85 amino acids) was determined by NMR, and the interaction between Tt alphaCTD and DNA with different sequences was investigated by means of chemical shift perturbation experiments. The tertiary structure of Tt alphaCTD is almost identical with that of Ec alphaCTD despite 32% sequence homology. However, Tt alphaCTD interacts with the upstream region sequence of the promoter in the Tt 16 S ribosomal protein operon rather than the Ec UP element DNA. The upstream region sequence of Tt is composed of 25 base pairs with 40% AT, unlike the Ec UP element with 80% AT. The DNA binding site in Tt alphaCTD is located on the surface composed of helix 4 and the loop preceding helix 4. The electric charges on this surface are not remarkably localized like those of Ec alphaCTD.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. A, comparison of the backbone of Tt CTD with that of Ec CTD. The backbones of Tt and Ec CTDs are given as a blue ribbon and red ribbon, respectively. The side chains of residues Phe^249, Trp321, and Ile^326 in Ec CTD form the hydrophobic core (6). B, a ribbon representation of the human BAF monomer ( 26). The green ribbons indicate the five helices (H1-H5).
Figure 7.
Fig. 7. Molecular surfaces of (A) Ec CTD and (B) Tt CTD. The molecular surfaces are colored according to the electrostatic potential; blue corresponds to a positive potential and red to a negative potential. Residues whose amide resonances were perturbed by the presence of DNA are connected by green lines (Ref. 6 and this study). Residues in Ec CTD connected by yellow lines are important for the interaction with the UP element in Ec CTD indicated by the Ala scan experiment (7). Residues Arg265 and Lys297 in Ec CTD correspond to Arg264 and Glu296 in Tt CTD, respectively, whose positions are shown in B. Their surfaces are viewed from the left side of the view shown in Fig. 4. These figures were calculated using the GRASP program (33).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 16057-16063) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18574242 N.Barinova, K.Kuznedelov, K.Severinov, and A.Kulbachinskiy (2008).
Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.
  J Biol Chem, 283, 22482-22489.  
16249335 K.J.Newberry, S.Nakano, P.Zuber, and R.G.Brennan (2005).
Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase.
  Proc Natl Acad Sci U S A, 102, 15839-15844.
PDB code: 1z3e
14872063 M.T.Marr, J.W.Roberts, S.E.Brown, M.Klee, and G.N.Gussin (2004).
Interactions among CII protein, RNA polymerase and the lambda PRE promoter: contacts between RNA polymerase and the -35 region of PRE are identical in the presence and absence of CII protein.
  Nucleic Acids Res, 32, 1083-1090.  
12756230 W.Ross, D.A.Schneider, B.J.Paul, A.Mertens, and R.L.Gourse (2003).
An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.
  Genes Dev, 17, 1293-1307.  
12426397 S.Singh, G.E.Folkers, A.M.Bonvin, R.Boelens, R.Wechselberger, A.Niztayev, and R.Kaptein (2002).
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
  EMBO J, 21, 6257-6266.
PDB code: 1kft
11812819 O.N.Ozoline, N.Fujita, and A.Ishihama (2001).
Mode of DNA-protein interaction between the C-terminal domain of Escherichia coli RNA polymerase alpha subunit and T7D promoter UP element.
  Nucleic Acids Res, 29, 4909-4919.  
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.