PDBsum entry 1a1d

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protein links
Nucleotidyltransferase PDB id
Protein chain
146 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
Name: Nucleotidyltransferase
Title: Yeast RNA polymerase subunit rpb8, nmr, minimized average structure, alpha carbons only
Structure: RNA polymerase. Chain: a. Fragment: subunit rpb8. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 1 models
Authors: S.Krapp,G.Kelly,J.Reischl,R.Weinzierl,S.Matthews
Key ref: S.Krapp et al. (1998). Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family. Nat Struct Biol, 5, 110-114. PubMed id: 9461075
10-Dec-97     Release date:   02-Mar-99    

Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
146 a.a.
146 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   5 terms 
  Biological process     transcription, RNA-dependent   7 terms 
  Biochemical function     RNA polymerase I activity     7 terms  


    Key reference    
Nat Struct Biol 5:110-114 (1998)
PubMed id: 9461075  
Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family.
S.Krapp, G.Kelly, J.Reischl, R.O.Weinzierl, S.Matthews.
RNA polymerase II subunit RPB8 is an essential subunit that is highly conserved throughout eukaryotic evolution and is present in all three types of nuclear RNA polymerases. We report the first high resolution structural insight into eukaryotic RNA polymerase architecture with the solution structure of RPB8 from Saccharomyces cerevisiae. It consists of an eight stranded, antiparallel beta-barrel, four short helical regions and a large, unstructured omega-loop. The strands are connected in classic Greek-key fashion. The overall topology is unusual and contains a striking C2 rotational symmetry. Furthermore, it is most likely a novel associate of the oligonucleotide/oligosaccharide (OB) binding protein class.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18081935 E.V.Koonin, K.S.Makarova, and J.G.Elkins (2007).
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".
  Biol Direct, 2, 38.  
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
16632472 X.Kang, Y.Hu, Y.Li, X.Guo, X.Jiang, L.Lai, B.Xia, and C.Jin (2006).
Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases.
  J Biol Chem, 281, 18216-18226.
PDB code: 2f3i
15671167 Bono, L.Riechmann, E.Girard, R.L.Williams, and G.Winter (2005).
A segment of cold shock protein directs the folding of a combinatorial protein.
  Proc Natl Acad Sci U S A, 102, 1396-1401.
PDB code: 2bh8
14963331 K.D.Westover, D.A.Bushnell, and R.D.Kornberg (2004).
Structural basis of transcription: separation of RNA from DNA by RNA polymerase II.
  Science, 303, 1014-1016.
PDB codes: 1r9r 1sfo
12145213 N.Bischler, L.Brino, C.Carles, M.Riva, H.Tschochner, V.Mallouh, and P.Schultz (2002).
Localization of the yeast RNA polymerase I-specific subunits.
  EMBO J, 21, 4136-4144.  
11486042 J.F.Briand, F.Navarro, P.Rematier, C.Boschiero, S.Labarre, M.Werner, G.V.Shpakovski, and P.Thuriaux (2001).
Partners of Rpb8p, a small subunit shared by yeast RNA polymerases I, II and III.
  Mol Cell Biol, 21, 6056-6065.  
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
10648788 M.Kimura, and A.Ishihama (2000).
Involvement of multiple subunit-subunit contacts in the assembly of RNA polymerase II.
  Nucleic Acids Res, 28, 952-959.  
10784442 P.Cramer, D.A.Bushnell, J.Fu, A.L.Gnatt, B.Maier-Davis, N.E.Thompson, R.R.Burgess, A.M.Edwards, P.R.David, and R.D.Kornberg (2000).
Architecture of RNA polymerase II and implications for the transcription mechanism.
  Science, 288, 640-649.
PDB code: 1en0
10384295 N.A.Woychik (1998).
Fractions to functions: RNA polymerase II thirty years later.
  Cold Spring Harb Symp Quant Biol, 63, 311-317.  
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.