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PDBsum entry 1hmj

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protein links
RNA polymerase PDB id
1hmj
Jmol
Contents
Protein chain
68 a.a. *
* Residue conservation analysis
PDB id:
1hmj
Name: RNA polymerase
Title: Solution structure of RNA polymerase subunit h
Structure: Protein (subunit h). Chain: a. Synonym: rpb5. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 1 models
Authors: A.Thiru,M.Hodach,J.Eloranta,V.Kostourou,R.Weinzierl
Key ref:
A.Thiru et al. (1999). RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes. J Mol Biol, 287, 753-760. PubMed id: 10191143 DOI: 10.1006/jmbi.1999.2638
Date:
05-Feb-99     Release date:   05-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q58443  (RPOH_METJA) -  DNA-directed RNA polymerase subunit H
Seq:
Struc:
78 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure

 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     transcription, DNA-dependent   1 term 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2638 J Mol Biol 287:753-760 (1999)
PubMed id: 10191143  
 
 
RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes.
A.Thiru, M.Hodach, J.J.Eloranta, V.Kostourou, R.O.Weinzierl, S.Matthews.
 
  ABSTRACT  
 
The archaeal H and eukaryotic RPB5 RNA polymerase subunits are highly homologous and are likely to play a fundamental role in transcription that extends from archaea to humans. We report the structure of subunit H, in solution, from the archaeon Methanococcus jannaschii using multidimensional nuclear magnetic resonance. The structure reveals a novel fold containing a four-stranded mixed beta sheet that is flanked on one side by three short helices. The dominant feature is beta-ribbon motif, which presents a hydrophobic, basic surface, and defines a general RNA polymerase architectural scaffold.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. A representation of the structural comparison of subunit H topology with other structures. (a) Subunit H; helices are shown as red tubes and strands as blue arrows. (b) RPB9; helices are shown as red tubes, strands as blue arrows and the zinc atom in light- blue. (c) CspB; helices are shown as red tubes, strands as blue arrows.
Figure 5.
Figure 5. (a) Ribbon representation of the subunit illustrating the extensive hydrophobic surface on the sol- vent exposed side of the b-sheet. Hydrophobic residues involved in domain interface contacts are shown; valine in blue, leucine in green, isoleucine in red and tyrosine in yellow. For clarity, the orientation has been flipped by 180 ° with respect to that in Figure 3 (a) and (c). (b) Ribbon representation of the subunit illustrating the extensive hydrophobic surface on the solvent-exposed side of the b-sheet. Hydrophobic residues involved in domain interface contacts are shown; valine in blue, leucine in green, isoleucine in red and tyrosine in yellow. The orientation is identical with that in Figure 3 (b) and (d). (c) GRASP (Nicholls et al., 1991) represen- tation of the electrostatic potential for the same orien- tation as (a). (d) GRASP (Nicholls et al., 1991) representation of the electrostatic potential for the same orientation as (b).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 753-760) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
11282478 S.D.Bell, and S.P.Jackson (2001).
Mechanism and regulation of transcription in archaea.
  Curr Opin Microbiol, 4, 208-213.  
10841538 A.Yee, V.Booth, A.Dharamsi, A.Engel, A.M.Edwards, and C.H.Arrowsmith (2000).
Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum.
  Proc Natl Acad Sci U S A, 97, 6311-6315.
PDB code: 1eik
10841537 F.Todone, R.O.Weinzierl, P.Brick, and S.Onesti (2000).
Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target.
  Proc Natl Acad Sci U S A, 97, 6306-6310.
PDB code: 1dzf
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.