PDBsum entry 1bdf

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protein Protein-protein interface(s) links
Nucleotidyltransferase PDB id
Protein chains
226 a.a. *
Waters ×239
* Residue conservation analysis
PDB id:
Name: Nucleotidyltransferase
Title: Structure of escherichia coli RNA polymerase alpha subunit n-terminal domain
Structure: RNA polymerase alpha subunit. Chain: a, b, c, d. Fragment: n-terminal domain residues 1-235. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Cell_line: bl-21. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl-21.
Biol. unit: Dimer (from PDB file)
2.50Å     R-factor:   0.225     R-free:   0.308
Authors: G.Zhang,S.A.Darst
Key ref:
G.Zhang and S.A.Darst (1998). Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science, 281, 262-266. PubMed id: 9657722 DOI: 10.1126/science.281.5374.262
08-May-98     Release date:   11-May-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha
329 a.a.
226 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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     DNA binding     3 terms  


DOI no: 10.1126/science.281.5374.262 Science 281:262-266 (1998)
PubMed id: 9657722  
Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain.
G.Zhang, S.A.Darst.
The 2.5 angstrom resolution x-ray crystal structure of the Escherichia coli RNA polymerase (RNAP) alpha subunit amino-terminal domain (alphaNTD), which is necessary and sufficient to dimerize and assemble the other RNAP subunits into a transcriptionally active enzyme and contains all of the sequence elements conserved among eukaryotic alpha homologs, has been determined. The alphaNTD monomer comprises two distinct, flexibly linked domains, only one of which participates in the dimer interface. In the alphaNTD dimer, a pair of helices from one monomer interact with the cognate helices of the other to form an extensive hydrophobic core. All of the determinants for interactions with the other RNAP subunits lie on one face of the alphaNTD dimer. Sequence alignments, combined with secondary-structure predictions, support proposals that a heterodimer of the eukaryotic RNAP subunits related to Saccharomyces cerevisiae Rpb3 and Rpb11 plays the role of the alphaNTD dimer in prokaryotic RNAP.
  Selected figure(s)  
Figure 1.
Fig. 1. Structure of the NTD dimer. (A) Schematic diagram showing the domain structure of E. coli RNAP (2). The black box indicates the NTD crystallized in this study ( residues 1 to 235). The gray boxes denote regions conserved in sequence between homologs of prokaryotic, archaebacterial, chloroplast, and eukaryotic^ RNAPs. (B) RIBBONS (28) diagram of the three-dimensional structure of the NTD dimer. One NTD monomer is colored green and the other is yellow. Unmodeled, disordered regions are indicated^ as dotted lines. (Top) View along the dimer twofold axis; (bottom) view perpendicular to the dimer twofold axis.
Figure 3.
Fig. 3. Dimer interface of NTD. Ribbon model, viewed along the dimer twofold axis, showing the conserved residues that form the hydrophobic^ core of the dimer interface (labeled on one monomer only). One^ NTD monomer is colored green, and the other is yellow. Helices H1 and H3 of each monomer are labeled. The figure was made with the program GRASP (29).
  The above figures are reprinted by permission from the AAAs: Science (1998, 281, 262-266) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21380560 S.Sato (2011).
The apicomplexan plastid and its evolution.
  Cell Mol Life Sci, 68, 1285-1296.  
  20856905 N.Opalka, J.Brown, W.J.Lane, K.A.Twist, R.Landick, F.J.Asturias, and S.A.Darst (2010).
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
  PLoS Biol, 8, 0.
PDB codes: 3lti 3lu0
20606261 S.Lara-González, J.J.Birktoft, and C.L.Lawson (2010).
Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain.
  Acta Crystallogr D Biol Crystallogr, 66, 806-812.
PDB code: 3k4g
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19903881 B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, and C.L.Lawson (2009).
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
  Proc Natl Acad Sci U S A, 106, 19830-19835.
PDB code: 3iyd
19580872 V.Lamour, L.F.Westblade, E.A.Campbell, and S.A.Darst (2009).
Crystal structure of the in vivo-assembled Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex.
  J Struct Biol, 168, 352-356.
PDB code: 3gfk
18203835 S.I.Husnain, and M.S.Thomas (2008).
The UP element is necessary but not sufficient for growth rate-dependent control of the Escherichia coli guaB promoter.
  J Bacteriol, 190, 2450-2457.  
17571921 J.C.Charity, M.M.Costante-Hamm, E.L.Balon, D.H.Boyd, E.J.Rubin, and S.L.Dove (2007).
Twin RNA polymerase-associated proteins control virulence gene expression in Francisella tularensis.
  PLoS Pathog, 3, e84.  
16039594 D.Jain, Y.Kim, K.L.Maxwell, S.Beasley, R.Zhang, G.N.Gussin, A.M.Edwards, and S.A.Darst (2005).
Crystal structure of bacteriophage lambda cII and its DNA complex.
  Mol Cell, 19, 259-269.
PDB codes: 1zpq 1zs4
15102444 C.L.Lawson, D.Swigon, K.S.Murakami, S.A.Darst, H.M.Berman, and R.H.Ebright (2004).
Catabolite activator protein: DNA binding and transcription activation.
  Curr Opin Struct Biol, 14, 10-20.  
15547256 J.Ma, and M.M.Howe (2004).
Binding of the C-terminal domain of the alpha subunit of RNA polymerase to the phage mu middle promoter.
  J Bacteriol, 186, 7858-7864.  
12954768 C.Sugiura, Y.Kobayashi, S.Aoki, C.Sugita, and M.Sugita (2003).
Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus.
  Nucleic Acids Res, 31, 5324-5331.  
12581657 K.S.Murakami, and S.A.Darst (2003).
Bacterial RNA polymerases: the wholo story.
  Curr Opin Struct Biol, 13, 31-39.  
12914698 N.Opalka, M.Chlenov, P.Chacon, W.J.Rice, W.Wriggers, and S.A.Darst (2003).
Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
  Cell, 114, 335-345.  
11861918 E.V.Sheveleva, N.V.Giordani, and R.B.Hallick (2002).
Identification and comparative analysis of the chloroplast alpha-subunit gene of DNA-dependent RNA polymerase from seven Euglena species.
  Nucleic Acids Res, 30, 1247-1254.  
12081950 M.C.Peck, T.Gaal, R.F.Fisher, R.L.Gourse, and S.R.Long (2002).
The RNA polymerase alpha subunit from Sinorhizobium meliloti can assemble with RNA polymerase subunits from Escherichia coli and function in basal and activated transcription both in vivo and in vitro.
  J Bacteriol, 184, 3808-3814.  
11839495 P.Cramer (2002).
Multisubunit RNA polymerases.
  Curr Opin Struct Biol, 12, 89-97.  
11904365 S.A.Darst, N.Opalka, P.Chacon, A.Polyakov, C.Richter, G.Zhang, and W.Wriggers (2002).
Conformational flexibility of bacterial RNA polymerase.
  Proc Natl Acad Sci U S A, 99, 4296-4301.  
  12167532 W.Park, C.O.Jeon, and E.L.Madsen (2002).
Interaction of NahR, a LysR-type transcriptional regulator, with the alpha subunit of RNA polymerase in the naphthalene degrading bacterium, Pseudomonas putida NCIB 9816-4.
  FEMS Microbiol Lett, 213, 159-165.  
11158566 L.Minakhin, S.Bhagat, A.Brunning, E.A.Campbell, S.A.Darst, R.H.Ebright, and K.Severinov (2001).
Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.
  Proc Natl Acad Sci U S A, 98, 892-897.
PDB code: 1hqm
11266593 N.Kannan, P.Chander, P.Ghosh, S.Vishveshwara, and D.Chatterji (2001).
Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.
  Protein Sci, 10, 46-54.  
11418764 R.Fedorov, V.Meshcheryakov, G.Gongadze, N.Fomenkova, N.Nevskaya, M.Selmer, M.Laurberg, O.Kristensen, S.Al-Karadaghi, A.Liljas, M.Garber, and S.Nikonov (2001).
Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.
  Acta Crystallogr D Biol Crystallogr, 57, 968-976.
PDB code: 1feu
11297923 S.A.Darst (2001).
Bacterial RNA polymerase.
  Curr Opin Struct Biol, 11, 155-162.  
11371534 S.M.Lohrke, H.Yang, and S.Jin (2001).
Reconstitution of acetosyringone-mediated Agrobacterium tumefaciens virulence gene expression in the heterologous host Escherichia coli.
  J Bacteriol, 183, 3704-3711.  
11987181 T.Heyduk, and A.Niedziela-Majka (2001).
Fluorescence resonance energy transfer analysis of escherichia coli RNA polymerase and polymerase-DNA complexes.
  Biopolymers, 61, 201-213.  
11600705 W.Meng, T.Belyaeva, N.J.Savery, S.J.Busby, W.E.Ross, T.Gaal, R.L.Gourse, and M.S.Thomas (2001).
UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker.
  Nucleic Acids Res, 29, 4166-4178.  
11046131 D.L.Pappas, and M.Hampsey (2000).
Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae.
  Mol Cell Biol, 20, 8343-8351.  
11029421 I.Artsimovitch, V.Svetlov, L.Anthony, R.R.Burgess, and R.Landick (2000).
RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro.
  J Bacteriol, 182, 6027-6035.  
  11111034 K.Nakasone, A.Ikegami, S.Fujii, C.Kato, and K.Horikoshi (2000).
Isolation and piezoresponse of the rpoA gene encoding the RNA polymerase alpha subunit from the deep-sea piezophilic bacterium Shewanella violacea.
  FEMS Microbiol Lett, 193, 261-268.  
10744988 K.Severinov (2000).
RNA polymerase structure-function: insights into points of transcriptional regulation.
  Curr Opin Microbiol, 3, 118-125.  
10821700 N.Fujita, S.Endo, and A.Ishihama (2000).
Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase.
  Biochemistry, 39, 6243-6249.  
  10673505 Q.Tan, K.L.Linask, R.H.Ebright, and N.A.Woychik (2000).
Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria.
  Genes Dev, 14, 339-348.  
11118218 R.D.Finn, E.V.Orlova, B.Gowen, M.Buck, and M.van Heel (2000).
Escherichia coli RNA polymerase core and holoenzyme structures.
  EMBO J, 19, 6833-6844.  
10972792 R.L.Gourse, W.Ross, and T.Gaal (2000).
UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition.
  Mol Microbiol, 37, 687-695.  
10747024 W.Meng, N.J.Savery, S.J.Busby, and M.S.Thomas (2000).
The Escherichia coli RNA polymerase alpha subunit linker: length requirements for transcription activation at CRP-dependent promoters.
  EMBO J, 19, 1555-1566.  
  10357858 B.Coulombe, and Z.F.Burton (1999).
DNA bending and wrapping around RNA polymerase: a "revolutionary" model describing transcriptional mechanisms.
  Microbiol Mol Biol Rev, 63, 457-478.  
  10198039 E.C.Nedea, D.Markov, T.Naryshkina, and K.Severinov (1999).
Localization of Escherichia coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature.
  J Bacteriol, 181, 2663-2665.  
10499798 G.Zhang, E.A.Campbell, L.Minakhin, C.Richter, K.Severinov, and S.A.Darst (1999).
Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.
  Cell, 98, 811-824.
PDB code: 1ddq
10075917 H.Raaijmakers, O.Vix, I.Törõ, S.Golz, B.Kemper, and D.Suck (1999).
X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture.
  EMBO J, 18, 1447-1458.
PDB code: 1en7
10047577 J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.
  Curr Opin Struct Biol, 9, 21-28.  
  10419950 S.M.Lohrke, S.Nechaev, H.Yang, K.Severinov, and S.J.Jin (1999).
Transcriptional activation of Agrobacterium tumefaciens virulence gene promoters in Escherichia coli requires the A. tumefaciens RpoA gene, encoding the alpha subunit of RNA polymerase.
  J Bacteriol, 181, 4533-4539.  
10384291 S.A.Darst, A.Polyakov, C.Richter, and G.Zhang (1998).
Structural studies of Escherichia coli RNA polymerase.
  Cold Spring Harb Symp Quant Biol, 63, 269-276.  
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.