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1l9z

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Revision as of 07:57, 25 November 2020

Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution

Structural highlights

1l9z is a 8 chain structure with sequence from Atcc 25104 and Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	rpoD (ATCC 25104)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RPOZ_THEAQ] 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.^[1] [Q9EZJ8_THEAQ] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.

Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.,Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA Science. 2002 May 17;296(5571):1285-90. PMID:12016307^[2]

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

References

↑ Minakhin L, Bhagat S, Brunning A, Campbell EA, Darst SA, Ebright RH, Severinov K. Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):892-7. PMID:11158566 doi:http://dx.doi.org/10.1073/pnas.98.3.892
↑ Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science. 2002 May 17;296(5571):1285-90. PMID:12016307 doi:10.1126/science.1069595

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l9z"

@@ Line 1: / Line 1: @@
 ==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==
-<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution|resolution]] 6.50&Aring;' scene=''>
+<StructureSection load='1l9z' size='340' side='right'caption='[[1l9z]], [[Resolution|resolution]] 6.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L9Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L9Z 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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 1l9z" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 40: @@
 [[Category: Atcc 25104]]
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Thermus aquaticus]]
 [[Category: Campbell, E A]]

1l9z

From Proteopedia

Revision as of 07:57, 25 November 2020

Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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