PDBsum entry 1dzf

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protein links
Transferase PDB id
Jmol PyMol
Protein chain
211 a.a. *
Waters ×169
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Rpb5 from s.Cerevisiae
Structure: DNA-directed RNA polymerases i, ii, and iii subun 1. Chain: a. Synonym: RNA polymerases i, ii, and iii subunit abc1, abc27 DNA-directed RNA polymerases i, ii, and iii 27 kda polypep engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: s288c. Cellular_location: nuclear. Gene: ybr154c or ybr1204. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: synthetic gene
Biol. unit: Monomer (from PDB file)
1.90Å     R-factor:   0.217     R-free:   0.271
Authors: F.Todone,R.O.J.Weinzierl,P.Brick,S.Onesti
Key ref:
F.Todone et al. (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. PubMed id: 10841537 DOI: 10.1073/pnas.97.12.6306
25-Feb-00     Release date:   09-Jun-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
215 a.a.
211 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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!
  Cellular component     nucleus   5 terms 
  Biological process     transcription, RNA-dependent   9 terms 
  Biochemical function     RNA polymerase I activity     7 terms  


DOI no: 10.1073/pnas.97.12.6306 Proc Natl Acad Sci U S A 97:6306-6310 (2000)
PubMed id: 10841537  
Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target.
F.Todone, R.O.Weinzierl, P.Brick, S.Onesti.
Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.
  Selected figure(s)  
Figure 3.
Fig. 3. (a) The C-terminal domain contains a number of residues that are highly conserved from archaea to humans. A cluster of invariant polar amino acids (mostly positively charged) are located on one surface of the domain. (b) The subunit interface contains few hydrophobic residues and is instead stabilized by polar interactions between a number of invariant residues in the N-terminal domain and Tyr 187 in the C-terminal domain. The figure shows the conserved residues at the interface and the hydrogen-bonding interactions. The secondary structure elements are colored as in Fig. 2.
Figure 4.
Fig. 4. Location of regions that have been proposed to interact with TFIIB and hepatitis B virus protein X (HBx). (a) Ribbon diagram representation of yRPB5 (in the same orientation as in Fig. 2). The fragment corresponding to the homologous sequence in hRPB5 that has been shown to interact with hTFIIB is shown in cyan whereas the region that is responsible for HBx interaction is shown in red. (b) Representation of the molecular surface of yRPB5 in the same orientation as Fig. 2 (Left) and rotated by 180° around the vertical axis (Right), showing the exposed surfaces of the above regions.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19141635 S.Lahmy, D.Pontier, E.Cavel, D.Vega, M.El-Shami, T.Kanno, and T.Lagrange (2009).
PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit.
  Proc Natl Acad Sci U S A, 106, 941-946.  
19419240 Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, and N.G.Abrescia (2009).
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
  PLoS Biol, 7, e102.
PDB codes: 2waq 2wb1
18573085 P.Cramer, K.J.Armache, S.Baumli, S.Benkert, F.Brueckner, C.Buchen, G.E.Damsma, S.Dengl, S.R.Geiger, A.J.Jasiak, A.Jawhari, S.Jennebach, T.Kamenski, H.Kettenberger, C.D.Kuhn, E.Lehmann, K.Leike, J.F.Sydow, and A.Vannini (2008).
Structure of eukaryotic RNA polymerases.
  Annu Rev Biophys, 37, 337-352.  
17179178 C.Zaros, J.F.Briand, Y.Boulard, S.Labarre-Mariotte, M.C.Garcia-Lopez, P.Thuriaux, and F.Navarro (2007).
Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
  Nucleic Acids Res, 35, 634-647.  
17267688 S.Devaux, S.Kelly, L.Lecordier, B.Wickstead, D.Perez-Morga, E.Pays, L.Vanhamme, and K.Gull (2007).
Diversification of function by different isoforms of conventionally shared RNA polymerase subunits.
  Mol Biol Cell, 18, 1293-1301.  
15985153 D.J.Rigden (2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
  BMC Struct Biol, 5, 9.  
15720711 M.Feder, and J.M.Bujnicki (2005).
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
  BMC Genomics, 6, 21.  
15684412 S.D.Pawlak, M.Radlinska, A.A.Chmiel, J.M.Bujnicki, and K.J.Skowronek (2005).
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII.
  Nucleic Acids Res, 33, 661-671.  
12737519 W.Wei, J.X.Gu, C.Q.Zhu, F.Y.Sun, D.Dorjsuren, Y.Lin, and S.Murakami (2003).
Interaction with general transcription factor IIF (TFIIF) is required for the suppression of activated transcription by RPB5-mediating protein (RMP).
  Cell Res, 13, 111-120.  
11846788 C.Schnarrenberger, and W.Martin (2002).
Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer.
  Eur J Biochem, 269, 868-883.  
11839495 P.Cramer (2002).
Multisubunit RNA polymerases.
  Curr Opin Struct Biol, 12, 89-97.  
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.