Transcription Termination Factor Rho: Difference between revisions

Latest revision as of 11:02, 21 February 2012

E. coli transcription termination factor Rho complex wit ssRNA and ANPPNP, 1pvo

Ligands:

Gene:

Related:

Structural annotation:
Resources:	InterPro : Ipr011112, Ipr011129, Ipr002110, Ipr000194, Ipr004665, Ipr003593, Ipr011113 Pfam : PF07498, PF00006, PF07497 SCOP : d1pvoa2, d1pvoa3, d1pvoa1, d1pvob1, d1pvob2, d1pvoc3, d1pvoc2, d1pvoc1, d1pvod2, d1pvod1, d1pvod3, d1pvoe3, d1pvoe2, d1pvoe1, d1pvof1, d1pvof3, d1pvof2 UniProt : P0AG30

Functional annotation:
Cellular component:	proton-transporting two-sector ATPase complex membrane fraction
Biological process:	transcription termination transcription regulation of transcription, DNA-dependent ATP synthesis coupled proton transport
Molecular function:	protein binding hydrogen ion transporting ATP synthase activity, rotational mechanism hydrogen ion transporting ATPase activity, rotational mechanism nucleotide binding helicase activity transcription termination factor activity RNA binding ATP binding nucleoside-triphosphatase activity hydrolase activity nucleic acid binding

Evolutionary conservation:

Toggle Conservation Colors:

Rows = identical sequences:

Further Information:

Caveats,

Explanation,
Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

Transcription termination factor Rho is a ring-shaped RNA-DNA helicase that induces release of transcription complexes at specific loci of bacterial genomes. Several structures of Rho in various liganded states haven been solved by X-ray crystallography by the J. M. Berger lab (Berkeley): 1a8v, 1pv4, 1pvo, 1xpr, 1xpu, 2a8v, and 2ht1.

The asymmetric unit solved as 2ht1 contains only two chains, so it represents only one third of the biological unit, which is a homo-hexamer. The scene here shows this homo-hexamer in a closed state ()^[1]. Note that this model has only the middle 324 amino acids in each chain, lacking the first 52 and the last 57 amino acids in each chain^[2].

In this model (), the Protein hexamer is bound to RNA, and some incidental "Solvent" (sulfate ions).

Here is one representation showing the same Rho hexamer in a closed state and with . In this scene, the foreground RNA is colored by element (C O N P). Also colored are Lys181, Lys283, Arg347, Arg353, and (in black) background RNA. See also Transcription and RNA Processing.

3D structures of helicase3D structures of helicase

Helicase

Additional ResourcesAdditional Resources

For additional information, see: Transcription and RNA Processing

NotesNotes

↑ File File:Rho1.pdb derived from 2ht1 by symmetry operations
↑ Missing residues can be found by aligning the PDB file's SEQRES records with the sequence of the residues assigned atomic coordinates, as listed by the S2C Server

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Marc Boudvillain, Eric Martz, David Canner, Michal Harel

[1] File File:Rho1.pdb derived from 2ht1 by symmetry operations

[2] Missing residues can be found by aligning the PDB file's SEQRES records with the sequence of the residues assigned atomic coordinates, as listed by the S2C Server

[1]

[2]

@@ Line 1: / Line 1: @@
-<applet load='Rho1.pdb' size='350' frame='true' align='right' scene='Transcription_Termination_Factor_Rho/Rho1_pdb_hexamer_overview/1' />
+{{STRUCTURE_1pvo|  PDB=1pvo  | SIZE=400| SCENE= |right|CAPTION=E. coli transcription termination factor Rho complex wit ssRNA and ANPPNP, [[1pvo]] }}
 '''Transcription termination factor Rho''' is a ring-shaped RNA-DNA '''helicase''' that induces release of transcription complexes at specific loci of bacterial genomes. Several structures of Rho in various liganded states haven been solved by X-ray crystallography by the J. M. Berger lab (Berkeley): [[1a8v]], [[1pv4]], [[1pvo]], [[1xpr]], [[1xpu]], [[2a8v]], and [[2ht1]].
-The [[Asymmetric Unit|asymmetric unit]] solved as [[2ht1]] contains only two chains, so it represents only one third of the [[Biological Unit|biological unit]], which is a homo-hexamer. The scene here shows this <scene name='Transcription_Termination_Factor_Rho/Rho1_pdb_hexamer_overview/1'>homo-hexamer in a closed state</scene> (file [[Image:Rho1.pdb]] derived from [2ht1]] by symmetry operations).
+The [[Asymmetric Unit|asymmetric unit]] solved as [[2ht1]] contains only two chains, so it represents only one third of the [[Biological Unit|biological unit]], which is a homo-hexamer. The scene here shows this homo-hexamer in a closed state (<scene name='Transcription_Termination_Factor_Rho/Rho1_pdb_hexamer_overview/1'>restore initial scene</scene>)<ref>File [[Image:Rho1.pdb]] derived from [[2ht1]] by symmetry operations</ref>. Note that this model has only the middle 324 amino acids in each chain, lacking the first 52 and the last 57 amino acids in each chain<ref>Missing residues can be found by aligning the PDB file's SEQRES records with the sequence of the residues assigned [[Atomic coordinate file|atomic coordinates]], as listed by the [http://bip.weizmann.ac.il/oca-bin/send-s2c?w=1&id=2HT1 S2C Server]</ref>.
+In this model (<scene name='Transcription_Termination_Factor_Rho/Rho1_pdb_hexamer_overview/2'>show composition</scene>), the {{Template:ColorKey Composition Protein}} hexamer is bound to {{Template:ColorKey Composition RNA}}, and some incidental "{{Template:ColorKey Composition Solvent}}" (sulfate ions).
+Here is one representation showing the same Rho hexamer in a closed state and with <scene name='Transcription_Termination_Factor_Rho/Rho_closed_1/3'>RNA fragments occupying both its primary and secondary binding sites</scene>. In this scene, the foreground RNA is colored by element
+({{Template:ColorKey_Element_C}}
+{{Template:ColorKey_Element_O}}
+{{Template:ColorKey_Element_N}}
+{{Template:ColorKey_Element_P}}). Also colored are
+<font color='#00a600'>'''Lys181'''</font>,
+<font color='#cc3700'>'''Lys283'''</font>,
+<font color='#20603c'>'''Arg347'''</font>,
+<font color='#974e94'>'''Arg353'''</font>, and (in black) '''background RNA'''.  See also [[Transcription and RNA Processing]].
+==3D structures of helicase==
+[[Helicase]]
+==Additional Resources==
+For additional information, see: [[Transcription and RNA Processing]]
+<br />
-Here is one representation showing the same Rho hexamer in a closed state and with <scene name='Transcription_Termination_Factor_Rho/Rho_closed_1/3'>RNA fragments occupying both its primary and secondary binding sites</scene>.
+==Notes==
+<references />