4xlp: Difference between revisions

Revision as of 10:37, 25 December 2019

Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter

Structural highlights

4xlp is a 16 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:	MG, ZN
Related:	4xln, 4xlq, 4xlr, 4xls, 4xax
Gene:	sigA (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] [SIGA_THEAQ] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]^[2] ^[3]

Publication Abstract from PubMed

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 A-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and sigma(A) dissociation.

Structure of a bacterial RNA polymerase holoenzyme open promoter complex.,Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08504. PMID:26349032^[4]

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:https://dx.doi.org/10.1073/pnas.98.3.892
↑ Minakhin L, Nechaev S, Campbell EA, Severinov K. Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol. 2001 Jan;183(1):71-6. PMID:11114902 doi:https://dx.doi.org/10.1128/JB.183.1.71-76.2001
↑ Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell. 2002 Mar;9(3):527-39. PMID:11931761
↑ Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08504. PMID:26349032 doi:https://dx.doi.org/10.7554/eLife.08504

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OCA

[1] 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:https://dx.doi.org/10.1073/pnas.98.3.892

[2] Minakhin L, Nechaev S, Campbell EA, Severinov K. Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol. 2001 Jan;183(1):71-6. PMID:11114902 doi:https://dx.doi.org/10.1128/JB.183.1.71-76.2001

[3] Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell. 2002 Mar;9(3):527-39. PMID:11931761

[4] Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08504. PMID:26349032 doi:https://dx.doi.org/10.7554/eLife.08504

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[2]

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@@ Line 1: / Line 1: @@
 ==Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter==
-<StructureSection load='4xlp' size='340' side='right' caption='[[4xlp]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
+<StructureSection load='4xlp' size='340' side='right'caption='[[4xlp]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xlp]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] 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=4XLP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XLP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xlp]] is a 16 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=4XLP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XLP 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">[[4xln|4xln]], [[4xlq|4xlq]], [[4xlr|4xlr]], [[4xls|4xls]], [[4xax|4xax]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sigA ([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=4xlp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xlp OCA], [http://pdbe.org/4xlp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xlp RCSB], [http://www.ebi.ac.uk/pdbsum/4xlp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xlp ProSAT]</span></td></tr>
@@ Line 20: / Line 21: @@
 </div>
 <div class="pdbe-citations 4xlp" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RNA polymerase|RNA polymerase]]
+*[[Sigma factor|Sigma factor]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Atcc 25104]]
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Thermus aquaticus]]
 [[Category: Bae, B]]

4xlp: Difference between revisions

Revision as of 10:37, 25 December 2019

Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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