PDBsum entry 1a62

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protein links
Transcription termination PDB id
Protein chain
125 a.a. *
Waters ×115
* Residue conservation analysis
PDB id:
Name: Transcription termination
Title: Crystal structure of the RNA-binding domain of the transcriptional terminator protein rho
Structure: Rho. Chain: a. Fragment: RNA binding domain, residues 1 - 130. Engineered: yes
Source: Escherichia coli bl21(de3). Organism_taxid: 469008. Strain: bl21 (de3). Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.55Å     R-factor:   0.216     R-free:   0.250
Authors: T.J.Allison,T.C.Wood,D.M.Briercheck,F.Rastinejad, J.P.Richardson,G.S.Rule
Key ref: T.J.Allison et al. (1998). Crystal structure of the RNA-binding domain from transcription termination factor rho. Nat Struct Biol, 5, 352-356. PubMed id: 9586995
05-Mar-98     Release date:   17-Jun-98    
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Protein chain
Pfam   ArchSchema ?
P0AG30  (RHO_ECOLI) -  Transcription termination factor Rho
419 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription termination, DNA-dependent   1 term 
  Biochemical function     nucleic acid binding     2 terms  


Nat Struct Biol 5:352-356 (1998)
PubMed id: 9586995  
Crystal structure of the RNA-binding domain from transcription termination factor rho.
T.J.Allison, T.C.Wood, D.M.Briercheck, F.Rastinejad, J.P.Richardson, G.S.Rule.
Transcription termination factor rho is an ATP-dependent hexameric helicase found in most eubacterial species. The Escherichia coli rho monomer consists of two domains, an RNA-binding domain (residues 1-130) and an ATPase domain (residues 131-419). The ATPase domain is homologous to the beta subunit of F1-ATPase. Here, we report that the crystal structure of the RNA-binding domain of rho (rho130) at 1.55 A confirms that rho130 contains the oligosaccharide/oligonucleotide-binding (OB) fold, a five stranded beta-barrel. The beta-barrel of rho130 is also surprisingly similar to the N-terminal beta-barrel of F1 ATPase, extending the applicability of F1 ATPase as a structural model for hexameric rho.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17400915 N.Sari, Y.He, V.Doseeva, K.Surabian, J.Ramprakash, F.Schwarz, O.Herzberg, and J.Orban (2007).
Solution structure of HI1506, a novel two-domain protein from Haemophilus influenzae.
  Protein Sci, 16, 977-982.
PDB code: 2out
17081977 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.
PDB code: 2ht1
16908525 T.K.Hitchens, Y.Zhan, L.V.Richardson, J.P.Richardson, and G.S.Rule (2006).
Sequence-specific interactions in the RNA-binding domain of Escherichia coli transcription termination factor Rho.
  J Biol Chem, 281, 33697-33703.  
15642265 E.Skordalakes, A.P.Brogan, B.S.Park, H.Kohn, and J.M.Berger (2005).
Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.
  Structure, 13, 99.
PDB codes: 1xpo 1xpr 1xpu
15576038 M.D.Tibbetts, E.N.Shiozaki, L.Gu, E.R.McDonald, W.S.El-Deiry, and Y.Shi (2004).
Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2.
  Structure, 12, 2257-2263.
PDB code: 1y02
15133049 S.Okubo, F.Hara, Y.Tsuchida, S.Shimotakahara, S.Suzuki, H.Hatanaka, S.Yokoyama, H.Tanaka, H.Yasuda, and H.Shindo (2004).
NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA oligomers.
  J Biol Chem, 279, 31455-31461.
PDB code: 1v66
14761943 X.Chen, and B.L.Stitt (2004).
The binding of C10 oligomers to Escherichia coli transcription termination factor Rho.
  J Biol Chem, 279, 16301-16310.  
14970217 Y.J.Jeong, D.E.Kim, and S.S.Patel (2004).
Nucleotide binding induces conformational changes in Escherichia coli transcription termination factor Rho.
  J Biol Chem, 279, 18370-18376.  
12598368 D.L.Theobald, R.M.Mitton-Fry, and D.S.Wuttke (2003).
Nucleic acid recognition by OB-fold proteins.
  Annu Rev Biophys Biomol Struct, 32, 115-133.  
12859904 E.Skordalakes, and J.M.Berger (2003).
Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading.
  Cell, 114, 135-146.
PDB codes: 1pv4 1pvo
14530440 G.Ziegelin, T.Niedenzu, R.Lurz, W.Saenger, and E.Lanka (2003).
Hexameric RSF1010 helicase RepA: the structural and functional importance of single amino acid residues.
  Nucleic Acids Res, 31, 5917-5929.
PDB code: 1olo
12887917 J.P.Richardson (2003).
Loading Rho to terminate transcription.
  Cell, 114, 157-159.  
11823434 A.C.Rodríguez, and D.Stock (2002).
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
  EMBO J, 21, 418-426.
PDB codes: 1gku 1gl9
11967078 V.C.Italiani, L.F.Zuleta, and M.V.Marques (2002).
The transcription termination factor Rho is required for oxidative stress survival in Caulobacter crescentus.
  Mol Microbiol, 44, 181-194.  
12034708 Y.Xu, H.Kohn, and W.R.Widger (2002).
Mutations in the rho transcription termination factor that affect RNA tracking.
  J Biol Chem, 277, 30023-30030.  
11329297 B.L.Stitt (2001).
Escherichia coli transcription termination factor Rho binds and hydrolyzes ATP using a single class of three sites.
  Biochemistry, 40, 2276-2281.  
11483577 L.Aravind, and E.V.Koonin (2001).
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system.
  Genome Res, 11, 1365-1374.  
11500367 M.Cai, Y.Huang, R.Ghirlando, K.L.Wilson, R.Craigie, and G.M.Clore (2001).
Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA.
  EMBO J, 20, 4399-4407.
PDB code: 1gjj
11459984 X.Yu, S.A.Jacobs, S.C.West, T.Ogawa, and E.H.Egelman (2001).
Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA.
  Proc Natl Acad Sci U S A, 98, 8419-8424.  
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
11701636 A.J.van Brabant, R.Stan, and N.A.Ellis (2000).
DNA helicases, genomic instability, and human genetic disease.
  Annu Rev Genomics Hum Genet, 1, 409-459.  
10678173 J.L.Battiste, T.V.Pestova, C.U.Hellen, and G.Wagner (2000).
The eIF1A solution structure reveals a large RNA-binding surface important for scanning function.
  Mol Cell, 5, 109-119.
PDB code: 1d7q
10892646 M.R.Singleton, M.R.Sawaya, T.Ellenberger, and D.B.Wigley (2000).
Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.
  Cell, 101, 589-600.
PDB codes: 1e0j 1e0k
10066795 A.Magyar, X.Zhang, F.Abdi, H.Kohn, and W.R.Widger (1999).
Identifying the bicyclomycin binding domain through biochemical analysis of antibiotic-resistant rho proteins.
  J Biol Chem, 274, 7316-7324.  
10206972 D.E.Kim, K.Shigesada, and S.S.Patel (1999).
Transcription termination factor Rho contains three noncatalytic nucleotide binding sites.
  J Biol Chem, 274, 11623-11628.  
10551822 D.E.Kim, and S.S.Patel (1999).
The mechanism of ATP hydrolysis at the noncatalytic sites of the transcription termination factor Rho.
  J Biol Chem, 274, 32667-32671.  
10404598 D.Fass, C.E.Bogden, and J.M.Berger (1999).
Crystal structure of the N-terminal domain of the DnaB hexameric helicase.
  Structure, 7, 691-698.
PDB code: 1b79
10404597 J.Weigelt, S.E.Brown, C.S.Miles, N.E.Dixon, and G.Otting (1999).
NMR structure of the N-terminal domain of E. coli DnaB helicase: implications for structure rearrangements in the helicase hexamer.
  Structure, 7, 681-690.
PDB code: 1jwe
10400475 S.Cusack (1999).
RNA-protein complexes.
  Curr Opin Struct Biol, 9, 66-73.  
10514525 S.Guo, S.Tabor, and C.C.Richardson (1999).
The linker region between the helicase and primase domains of the bacteriophage T7 gene 4 protein is critical for hexamer formation.
  J Biol Chem, 274, 30303-30309.  
10049334 T.C.Mou, C.W.Gray, and D.M.Gray (1999).
The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate.
  Biophys J, 76, 1537-1551.  
9587002 D.M.Briercheck, T.C.Wood, T.J.Allison, J.P.Richardson, and G.S.Rule (1998).
The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions.
  Nat Struct Biol, 5, 393-399.
PDB code: 1a63
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.