PDBsum entry 1eik

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protein links
Transferase PDB id
Protein chain
77 a.a. *
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Solution structure of RNA polymerase subunit rpb5 from methanobacterium thermoautotrophicum
Structure: RNA polymerase subunit rpb5. Chain: a. Engineered: yes
Source: Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 10 models
Authors: A.Yee,V.Booth,A.Dharamsi,A.Engel,A.M.Edwards,C.H.Arrowsmith, Northeast Structural Genomics Consortium (Nesg)
Key ref:
A.Yee et al. (2000). Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum. Proc Natl Acad Sci U S A, 97, 6311-6315. PubMed id: 10841538 DOI: 10.1073/pnas.97.12.6311
25-Feb-00     Release date:   21-Jun-00    
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Protein chain
Pfam   ArchSchema ?
O27122  (RPOH_METTH) -  DNA-directed RNA polymerase subunit H
77 a.a.
77 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   1 term 
  Biochemical function     transferase activity     4 terms  


DOI no: 10.1073/pnas.97.12.6311 Proc Natl Acad Sci U S A 97:6311-6315 (2000)
PubMed id: 10841538  
Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum.
A.Yee, V.Booth, A.Dharamsi, A.Engel, A.M.Edwards, C.H.Arrowsmith.
RPB5 is an essential subunit of eukaryotic and archaeal RNA polymerases. It is a proposed target for transcription activator proteins in eukaryotes, but the mechanism of interaction is not known. We have determined the solution structure of the RPB5 subunit from the thermophilic archeon, Methanobacterium thermoautotrophicum. MtRBP5 contains a four-stranded beta-sheet platform supporting two alpha-helices, one on each side of the beta-sheet, resulting in an overall mushroom shape that does not appear to have any structural homologues in the structural database. The position and conservation of charged surface residues suggests possible modes of interaction with other proteins, as well as a rationale for the thermal stability of this protein.
  Selected figure(s)  
Figure 2.
Fig. 2. NMR-derived structure of mtRPB5. (A) Ribbon diagram of a representative structure. (B) The backbone trace of the 10 lowest energy structures superimposed from residue 12 to 77. Drawn in blue are the solvent-inaccessible sidechains that form the hydrophobic core. The -strands are cyan, and helices are red. Diagrams were created by using MOLMOL (33).
Figure 3.
Fig. 3. Strips from the three-dimensional 13C-edited NOESY in D[2]O at the carbon planes corresponding to the C 2 position of Val 25 (19.6 ppm), and the C (131.9 ppm), and C (116.3 ppm) of Tyr 72 showing unambiguous NOEs between the Tyr 72 and Val 25.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
18235446 A.Hirata, B.J.Klein, and K.S.Murakami (2008).
The X-ray crystal structure of RNA polymerase from Archaea.
  Nature, 451, 851-854.
PDB codes: 2pa8 2pmz 3hkz
16937244 M.Revington, A.Semesi, A.Yee, C.H.Arrowsmith, and G.S.Shaw (2006).
The solution structure of the protein ydhA from Escherichia coli.
  J Biomol NMR, 35, 295-300.  
16260765 M.Revington, A.Semesi, A.Yee, and G.S.Shaw (2005).
Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase.
  Protein Sci, 14, 3115-3120.
PDB code: 2asy
14973185 A.Paz, D.Mester, I.Baca, E.Nevo, and A.Korol (2004).
Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes.
  Proc Natl Acad Sci U S A, 101, 2951-2956.  
11470603 P.R.Mittl, and M.G.Grütter (2001).
Structural genomics: opportunities and challenges.
  Curr Opin Chem Biol, 5, 402-408.  
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
11058130 F.Werner, J.J.Eloranta, and R.O.Weinzierl (2000).
Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12.
  Nucleic Acids Res, 28, 4299-4305.  
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.