PDBsum entry 1a62

Transcription termination

PDB id

1a62

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Contents

			Protein chain

					125 a.a. *

			Waters ×115

* Residue conservation analysis

PDB id:

1a62

Links

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.

Resolution:

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

Date:

05-Mar-98

Release date:

17-Jun-98

PROCHECK

	Headers

	References

Protein chain

P0AG30 (RHO_ECOLI) - Transcription termination factor Rho from Escherichia coli (strain K12)

Seq: Struc:					419 a.a. 125 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.6.4.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	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.

ABSTRACT

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.