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3aoi

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Revision as of 11:55, 4 August 2016

RNA polymerase-Gfh1 complex (Crystal type 2)

Structural highlights

3aoi is a 24 chain structure with sequence from Thet8 and Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3aoh
Gene:	TTHA1042 (THET8)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RPOZ_THET8] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOC_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [GFH1_THET8] Inhibits all catalytic activities of RNA polymerase (RNAP) by partially occluding its substrate-binding site and preventing NTP binding.^[1] ^[2] ^[3] [RPOB_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Publication Abstract from PubMed

The multi-subunit DNA-dependent RNA polymerase (RNAP) is the principal enzyme of transcription for gene expression. Transcription is regulated by various transcription factors. Gre factor homologue 1 (Gfh1), found in the Thermus genus, is a close homologue of the well-conserved bacterial transcription factor GreA, and inhibits transcription initiation and elongation by binding directly to RNAP. The structural basis of transcription inhibition by Gfh1 has remained elusive, although the crystal structures of RNAP and Gfh1 have been determined separately. Here we report the crystal structure of Thermus thermophilus RNAP complexed with Gfh1. The amino-terminal coiled-coil domain of Gfh1 fully occludes the channel formed between the two central modules of RNAP; this channel would normally be used for nucleotide triphosphate (NTP) entry into the catalytic site. Furthermore, the tip of the coiled-coil domain occupies the NTP beta-gamma phosphate-binding site. The NTP-entry channel is expanded, because the central modules are 'ratcheted' relative to each other by approximately 7 degrees , as compared with the previously reported elongation complexes. This 'ratcheted state' is an alternative structural state, defined by a newly acquired contact between the central modules. Therefore, the shape of Gfh1 is appropriate to maintain RNAP in the ratcheted state. Simultaneously, the ratcheting expands the nucleic-acid-binding channel, and kinks the bridge helix, which connects the central modules. Taken together, the present results reveal that Gfh1 inhibits transcription by preventing NTP binding and freezing RNAP in the alternative structural state. The ratcheted state might also be associated with other aspects of transcription, such as RNAP translocation and transcription termination.

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.,Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S Nature. 2010 Dec 16;468(7326):978-82. Epub 2010 Dec 1. PMID:21124318^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hogan BP, Hartsch T, Erie DA. Transcript cleavage by Thermus thermophilus RNA polymerase. Effects of GreA and anti-GreA factors. J Biol Chem. 2002 Jan 11;277(2):967-75. Epub 2001 Oct 17. PMID:11606592 doi:http://dx.doi.org/10.1074/jbc.M108737200
↑ Laptenko O, Borukhov S. Biochemical assays of Gre factors of Thermus thermophilus. Methods Enzymol. 2003;371:219-32. PMID:14712703 doi:http://dx.doi.org/10.1016/S0076-6879(03)71016-7
↑ Symersky J, Perederina A, Vassylyeva MN, Svetlov V, Artsimovitch I, Vassylyev DG. Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J Biol Chem. 2006 Jan 20;281(3):1309-12. Epub 2005 Nov 18. PMID:16298991 doi:10.1074/jbc.C500405200
↑ Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature. 2010 Dec 16;468(7326):978-82. Epub 2010 Dec 1. PMID:21124318 doi:10.1038/nature09573

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3aoi"

@@ Line 1: / Line 1: @@
 ==RNA polymerase-Gfh1 complex (Crystal type 2)==
 <StructureSection load='3aoi' size='340' side='right' caption='[[3aoi]], [[Resolution|resolution]] 4.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3aoi]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AOI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AOI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3aoi]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AOI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AOI FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aoh|3aoh]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA1042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA1042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3aoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aoi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3aoi RCSB], [http://www.ebi.ac.uk/pdbsum/3aoi PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3aoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aoi OCA], [http://pdbe.org/3aoi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aoi RCSB], [http://www.ebi.ac.uk/pdbsum/3aoi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aoi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[http://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/Q5SJG6_THET8 Q5SJG6_THET8]] Inhibits all catalytic activities of RNA polymerase (RNAP) by partially occluding its substrate-binding site and preventing NTP binding.<ref>PMID:11606592</ref> <ref>PMID:14712703</ref> <ref>PMID:16298991</ref>  [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
+[[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[http://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/GFH1_THET8 GFH1_THET8]] Inhibits all catalytic activities of RNA polymerase (RNAP) by partially occluding its substrate-binding site and preventing NTP binding.<ref>PMID:11606592</ref> <ref>PMID:14712703</ref> <ref>PMID:16298991</ref>  [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3aoi" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 28: / Line 30: @@
 [[Category: DNA-directed RNA polymerase]]
 [[Category: Thermus thermophilus]]
+[[Category: Thet8]]
 [[Category: Kumarevel, T]]
 [[Category: Structural genomic]]

3aoi

From Proteopedia

Revision as of 11:55, 4 August 2016

RNA polymerase-Gfh1 complex (Crystal type 2)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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