PDBsum entry 1ef4

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protein metals links
Transferase PDB id
Protein chain
55 a.a. *
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Solution structure of the essential RNA polymerase subunit rpb10 from methanobacterium thermoautotrophicum
Structure: DNA-directed RNA polymerase. Chain: a. Fragment: subunit rpb10. Synonym: subunit n. Engineered: yes
Source: Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: C.D.Mackereth,C.H.Arrowsmith,A.M.Edwards,L.P.Mcintosh, Northeast Structural Genomics Consortium (Nesg)
Key ref:
C.D.Mackereth et al. (2000). Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum. Proc Natl Acad Sci U S A, 97, 6316-6321. PubMed id: 10841539 DOI: 10.1073/pnas.97.12.6316
07-Feb-00     Release date:   14-Jun-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O26147  (RPON_METTH) -  DNA-directed RNA polymerase subunit N
55 a.a.
55 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!
  Biological process     transcription, DNA-dependent   1 term 
  Biochemical function     transferase activity     6 terms  


DOI no: 10.1073/pnas.97.12.6316 Proc Natl Acad Sci U S A 97:6316-6321 (2000)
PubMed id: 10841539  
Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
C.D.Mackereth, C.H.Arrowsmith, A.M.Edwards, L.P.McIntosh.
The RNA polymerase subunit RPB10 displays a high level of conservation across archaea and eukarya and is required for cell viability in yeast. Structure determination of this RNA polymerase subunit from Methanobacterium thermoautotrophicum reveals a topology, which we term a zinc-bundle, consisting of three alpha-helices stabilized by a zinc ion. The metal ion is bound within an atypical CX(2)CX(n)CC sequence motif and serves to bridge an N-terminal loop with helix 3. This represents an example of two adjacent zinc-binding Cys residues within an alpha-helix conformation. Conserved surface features of RPB10 include discrete regions of neutral, acidic, and basic residues, the latter being located around the zinc-binding site. One or more of these regions may contribute to the role of this subunit as a scaffold protein within the polymerase holoenzyme.
  Selected figure(s)  
Figure 2.
Fig. 2. NMR-derived zinc-bundle structure of mtRPB10. (A) The -trace of 20 structures of mtRBP10, superimposed by using the main chain helical atoms (14-26, 30-37, and 42-48). The helices are highlighted in red, and the zinc ion is shown as a pink ball. Every tenth residue is numbered. The N- and C-terminal residues Met1, Ile2, Glu53, Thr54, and Trp55 are conformationally flexible in solution, as evident by heteronuclear 1H{15N} NOE values less than 0.5. (B) Zinc binding site in mtRPB10. (C) Stereo view of a representative mtRPB10 structure displaying residues within the hydrophobic core: Leu7 and Val13 in the N-terminal region, Phe17, Tyr20, and Val24 of helix 1, Pro30, Val33, Leu34, and Leu37 of helix 2, Leu39 in the loop between helix 2 and 3, Leu48, Ile49 of helix 3, and Val52 in the C-terminal region. These conserved residues are shown according to the color scheme of Fig. 1.
Figure 4.
Fig. 4. Structural similarity to protein and nucleic acid binding domains. mtRPB10 is shown with helices 1, 2, and 3 colored red, green, and blue, respectively. The zinc atom is shown as a pink ball. This color scheme is used to identify similar helices in the following structurally related proteins found in the Protein Data Bank: the protein-binding N-terminal domain of HIV-2 integrase (PDB ID code 1AUB), with the zinc-chelating Cys and His residues drawn in light gray, and the zinc atom shown as a pink ball; the DNA-binding homeodomain of engrailed (PDB ID code 1ENH); and the RNA-binding domain of ribosome subunit L11 (PDB ID code 1QA6).
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15466049 E.L.Hendrickson, R.Kaul, Y.Zhou, D.Bovee, P.Chapman, J.Chung, E.Conway de Macario, J.A.Dodsworth, W.Gillett, D.E.Graham, M.Hackett, A.K.Haydock, A.Kang, M.L.Land, R.Levy, T.J.Lie, T.A.Major, B.C.Moore, I.Porat, A.Palmeiri, G.Rouse, C.Saenphimmachak, D.Söll, S.Van Dien, T.Wang, W.B.Whitman, Q.Xia, Y.Zhang, F.W.Larimer, M.V.Olson, and J.A.Leigh (2004).
Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.
  J Bacteriol, 186, 6956-6969.  
15155190 V.Dixit, E.Bini, M.Drozda, and P.Blum (2004).
Mercury inactivates transcription and the generalized transcription factor TFB in the archaeon Sulfolobus solfataricus.
  Antimicrob Agents Chemother, 48, 1993-1999.  
14517549 J.Zhou, and Z.Xu (2003).
Structural determinants of SecB recognition by SecA in bacterial protein translocation.
  Nat Struct Biol, 10, 942-947.
PDB code: 1ozb
11179890 J.H.Laity, B.M.Lee, and P.E.Wright (2001).
Zinc finger proteins: new insights into structural and functional diversity.
  Curr Opin Struct Biol, 11, 39-46.  
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.  
11282478 S.D.Bell, and S.P.Jackson (2001).
Mechanism and regulation of transcription in archaea.
  Curr Opin Microbiol, 4, 208-213.  
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 code is shown on the right.