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PDBsum entry 2ht1

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protein dna_rna ligands Protein-protein interface(s) links
Hydrolase/RNA PDB id
2ht1
Jmol PyMol
Contents
Protein chains
324 a.a. *
DNA/RNA
Ligands
__U-__C ×2
SO4 ×2
* Residue conservation analysis
PDB id:
2ht1
Name: Hydrolase/RNA
Title: The closed ring structure of the rho transcription terminati in complex with nucleic acid in the motor domains
Structure: 5'-r( Up C)-3'. Chain: j, k. Engineered: yes. 5'-r( Up Cp Up Cp U)-3'. Chain: m. Engineered: yes. Transcription termination factor rho. Chain: a, b. Synonym: atp-dependent helicase rho.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: rho, nita, psua, rnsc, sbaa, tsu. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PDB file)
Resolution:
3.51Å     R-factor:   0.287     R-free:   0.328
Authors: E.Skordalakes,J.M.Berger
Key ref:
E.Skordalakes and J.M.Berger (2006). Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell, 127, 553-564. PubMed id: 17081977 DOI: 10.1016/j.cell.2006.08.051
Date:
24-Jul-06     Release date:   14-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AG30  (RHO_ECOLI) -  Transcription termination factor Rho
Seq:
Struc:
419 a.a.
324 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     transcription, DNA-dependent   3 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
DOI no: 10.1016/j.cell.2006.08.051 Cell 127:553-564 (2006)
PubMed id: 17081977  
 
 
Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor.
E.Skordalakes, J.M.Berger.
 
  ABSTRACT  
 
Hexameric helicases and translocases are required for numerous essential nucleic-acid transactions. To better understand the mechanisms by which these enzymes recognize target substrates and use nucleotide hydrolysis to power molecular movement, we have determined the structure of the Rho transcription termination factor, a hexameric RNA/DNA helicase, with single-stranded RNA bound to the motor domains of the protein. The structure reveals a closed-ring "trimer of dimers" conformation for the hexamer that contains an unanticipated arrangement of conserved loops required for nucleic-acid translocation. RNA extends across a shallow intersubunit channel formed by conserved amino acids required for RNA-stimulated ATP hydrolysis and translocation and directly contacts a conserved lysine, just upstream of the catalytic GKT triad, in the phosphate-binding (P loop) motif of the ATP-binding pocket. The structure explains the molecular effects of numerous mutations and provides new insights into the links between substrate recognition, ATP turnover, and coordinated strand movement.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Rho Protomer Structure
Figure 3.
Figure 3. Primary and Secondary RNA-Binding Sites of Rho
 
  The above figures are reprinted by permission from Cell Press: Cell (2006, 127, 553-564) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20219473 I.Cuesta, R.Núñez-Ramírez, S.H.Scheres, D.Gai, X.S.Chen, E.Fanning, and J.M.Carazo (2010).
Conformational rearrangements of SV40 large T antigen during early replication events.
  J Mol Biol, 397, 1276-1286.  
20722407 P.Jing, F.Haque, D.Shu, C.Montemagno, and P.Guo (2010).
One-way traffic of a viral motor channel for double-stranded DNA translocation.
  Nano Lett, 10, 3620-3627.  
20075920 V.Epshtein, D.Dutta, J.Wade, and E.Nudler (2010).
An allosteric mechanism of Rho-dependent transcription termination.
  Nature, 463, 245-249.  
19915588 A.Schwartz, M.Rabhi, F.Jacquinot, E.Margeat, A.R.Rahmouni, and M.Boudvillain (2009).
A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase.
  Nat Struct Mol Biol, 16, 1309-1316.  
19217392 B.Bae, Y.H.Chen, A.Costa, S.Onesti, J.S.Brunzelle, Y.Lin, I.K.Cann, and S.K.Nair (2009).
Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog.
  Structure, 17, 211-222.
PDB code: 3f8t
19129763 J.R.Moffitt, Y.R.Chemla, K.Aathavan, S.Grimes, P.J.Jardine, D.L.Anderson, and C.Bustamante (2009).
Intersubunit coordination in a homomeric ring ATPase.
  Nature, 457, 446-450.  
19450514 K.R.Simonetta, S.L.Kazmirski, E.R.Goedken, A.J.Cantor, B.A.Kelch, R.McNally, S.N.Seyedin, D.L.Makino, M.O'Donnell, and J.Kuriyan (2009).
The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
  Cell, 137, 659-671.
PDB codes: 3glf 3glg 3glh 3gli
19946136 M.L.Bochman, and A.Schwacha (2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
  Microbiol Mol Biol Rev, 73, 652-683.  
19879839 N.D.Thomsen, and J.M.Berger (2009).
Running in reverse: the structural basis for translocation polarity in hexameric helicases.
  Cell, 139, 523-534.
PDB code: 3ice
19914167 S.E.Glynn, A.Martin, A.R.Nager, T.A.Baker, and R.T.Sauer (2009).
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
  Cell, 139, 744-756.
PDB codes: 3hte 3hws
19837672 X.Chen, and B.L.Stitt (2009).
ADP but not P(i) dissociation contributes to rate limitation for Escherichia coli Rho.
  J Biol Chem, 284, 33773-33780.  
18650940 A.Costa, G.van Duinen, B.Medagli, J.Chong, N.Sakakibara, Z.Kelman, S.K.Nair, A.Patwardhan, and S.Onesti (2008).
Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase.
  EMBO J, 27, 2250-2258.  
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
18487194 C.J.Cardinale, R.S.Washburn, V.R.Tadigotla, L.M.Brown, M.E.Gottesman, and E.Nudler (2008).
Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli.
  Science, 320, 935-938.  
18482981 D.Dutta, J.Chalissery, and R.Sen (2008).
Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA.
  J Biol Chem, 283, 20243-20251.  
18057007 D.E.Kainov, E.J.Mancini, J.Telenius, J.Lísal, J.M.Grimes, D.H.Bamford, D.I.Stuart, and R.Tuma (2008).
Structural basis of mechanochemical coupling in a hexameric molecular motor.
  J Biol Chem, 283, 3607-3617.
PDB codes: 2vhc 2vhj 2vhq 2vht 2vhu
18729732 J.W.Roberts, S.Shankar, and J.J.Filter (2008).
RNA polymerase elongation factors.
  Annu Rev Microbiol, 62, 211-233.  
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
17724015 A.Schwartz, E.Margeat, A.R.Rahmouni, and M.Boudvillain (2007).
Transcription termination factor rho can displace streptavidin from biotinylated RNA.
  J Biol Chem, 282, 31469-31476.  
17938630 A.Y.Mulkidjanian, K.S.Makarova, M.Y.Galperin, and E.V.Koonin (2007).
Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.
  Nat Rev Microbiol, 5, 892-899.  
17599352 J.Chalissery, S.Banerjee, I.Bandey, and R.Sen (2007).
Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex.
  J Mol Biol, 371, 855-872.  
17157498 K.P.Hopfner, and J.Michaelis (2007).
Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics.
  Curr Opin Struct Biol, 17, 87-95.  
17565995 P.Gutiérrez, G.Kozlov, L.Gabrielli, D.Elias, M.J.Osborne, I.E.Gallouzi, and K.Gehring (2007).
Solution structure of YaeO, a Rho-specific inhibitor of transcription termination.
  J Biol Chem, 282, 23348-23353.
PDB code: 1sg5
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.

 

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