PDBsum entry 3bmb

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RNA binding protein PDB id
Protein chains
135 a.a. *
SO4 ×10
_CL ×2
Waters ×278
* Residue conservation analysis
PDB id:
Name: RNA binding protein
Title: Crystal structure of a new RNA polymerase interacting protein
Structure: Regulator of nucleoside diphosphate kinase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: rnk. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.91Å     R-factor:   0.213     R-free:   0.237
Authors: S.A.Darst,V.Lamour
Key ref:
V.Lamour et al. (2008). Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein. J Mol Biol, 383, 367-379. PubMed id: 18760284 DOI: 10.1016/j.jmb.2008.08.011
12-Dec-07     Release date:   28-Oct-08    
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Protein chains
Pfam   ArchSchema ?
P0AFW4  (RNK_ECOLI) -  Regulator of nucleoside diphosphate kinase
136 a.a.
135 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biological regulation   2 terms 
  Biochemical function     protein binding     3 terms  


DOI no: 10.1016/j.jmb.2008.08.011 J Mol Biol 383:367-379 (2008)
PubMed id: 18760284  
Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein.
V.Lamour, S.T.Rutherford, K.Kuznedelov, U.A.Ramagopal, R.L.Gourse, K.Severinov, S.A.Darst.
Sequence-based searches identified a new family of genes in proteobacteria, named rnk, which shares high sequence similarity with the C-terminal domains of the Gre factors (GreA and GreB) and the Thermus/Deinococcus anti-Gre factor Gfh1. We solved the X-ray crystal structure of Escherichia coli regulator of nucleoside kinase (Rnk) at 1.9 A resolution using the anomalous signal from the native protein. The Rnk structure strikingly resembles those of E. coli GreA and GreB and Thermus Gfh1, all of which are RNA polymerase (RNAP) secondary channel effectors and have a C-terminal domain belonging to the FKBP fold. Rnk, however, has a much shorter N-terminal coiled coil. Rnk does not stimulate transcript cleavage in vitro, nor does it reduce the lifetime of the complex formed by RNAP on promoters. We show that Rnk competes with the Gre factors and DksA (another RNAP secondary channel effector) for binding to RNAP in vitro, and although we found that the concentration of Rnk in vivo was much lower than that of DksA, it was similar to that of GreB, consistent with a potential regulatory role for Rnk as an anti-Gre factor.
  Selected figure(s)  
Figure 2.
Fig. 2. Rnk interdomain orientation. (a) Ec Rnk (red) superposition with Ec GreA (yellow^10) and Taq Gfh1.^23 The structures have been superimposed on the C-terminal FKBP domain. The Rnk coiled coil is rotated 104° away from the coiled-coil position observed in Ec GreA. The Rnk coiled coil is 22 Å shorter than the GreA and Gfh1 coiled coils. (b) Ec Rnk interdomain hydrogen bond network. Side chains of N-terminal residues Arg3, Asn9, and Asp12 interact with amino acids Thr55, Tyr77, Leu99, and Glu129 of the C-terminal FKBP domain. Fig. S2. (a) Rnk crystal asymmetric unit content. The two Rnk molecules in the asymmetric unit appear in gray. Five sulfate ions per molecule are bound to surface arginines. Chloride ions are located in a hydrophobic pocket at the tip of the coiled coil. (b) FKBP domain flexible loops. Ec Rnk, Ec GreA ,and Taq Gfh1 are superposed on their C-terminal FKBP domain. Flexible loops are colored red (Rnk), yellow (GreA), and cyan (Gfh1). The GreA loop appearing as a dotted line was disordered in the crystal structure.[628]^10 The flexibility in this particular loop might allow conserved residues in the FKBP domain to face the RNAP β′ coiled coil.
Figure 6.
Fig. 6. Potential RNAP binding surface of Rnk. (a) Rnk C-terminal FKBP domain conserved residues. Conserved residues in the Rnk family (see alignment Fig. S1) are highlighted (left) on the RNK structure (worm representation with NTD in yellow and FKBP domain in orange) and (right) in a molecular surface representation colored according to the BLOSUM score.
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 383, 367-379) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20008510 K.Potrykus, H.Murphy, X.Chen, J.A.Epstein, and M.Cashel (2010).
Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL.
  Nucleic Acids Res, 38, 1636-1651.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
19424178 M.D.Blankschien, J.H.Lee, E.D.Grace, C.W.Lennon, J.A.Halliday, W.Ross, R.L.Gourse, and C.Herman (2009).
Super DksAs: substitutions in DksA enhancing its effects on transcription initiation.
  EMBO J, 28, 1720-1731.  
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