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6eec

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Revision as of 00:24, 11 April 2020

Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin

6eec, resolution 3.55Å

Structural highlights

6eec is a 10 chain structure with sequence from "bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	rpoA ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoB, SAMEA2682864_01701 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoC ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), sigA, mysA, rpoD, rpoV ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rbpA ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), carD ("Bacillus tuberculosis" (Zopf 1883) Klein 1884)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RBPA_MYCTO] Binds to RNA polymerase (RNAP), stimulating transcription from principal, but not alternative sigma factor promoters. [RPOC_MYCTA] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [CARD_MYCTO] Controls rRNA transcription by binding to the RNA polymerase (RNAP). Required for replication and persistence during infection of mice (By similarity). [V9Z879_MYCTX] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [RPOA_MYCTA] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [A0A0T9N9K3_MYCTX] 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.[HAMAP-Rule:MF_00366][SAAS:SAAS00298387] [SIGA_MYCTO] 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]

Publication Abstract from PubMed

A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex(1-3). To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed(4-6). Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates. The structures show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 and switch 2-universal structural features of RNAP-in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of fork-loop 2 and switch 2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression across all domains of life.

Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.,Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA Nature. 2019 Jan;565(7739):382-385. doi: 10.1038/s41586-018-0840-5. Epub 2019 Jan, 9. PMID:30626968^[1]

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

References

↑ Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA. Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. Nature. 2019 Jan;565(7739):382-385. doi: 10.1038/s41586-018-0840-5. Epub 2019 Jan, 9. PMID:30626968 doi:http://dx.doi.org/10.1038/s41586-018-0840-5

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/6eec"

@@ Line 3: / Line 3: @@
 <SX load='6eec' size='340' side='right' viewer='molstar' caption='[[6eec]], [[Resolution|resolution]] 3.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6eec]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6eec]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6EEC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoB, SAMEA2682864_01701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), sigA, mysA, rpoD, rpoV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), carD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6eec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eec OCA], [http://pdbe.org/6eec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eec RCSB], [http://www.ebi.ac.uk/pdbsum/6eec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eec 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=6eec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eec OCA], [http://pdbe.org/6eec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eec RCSB], [http://www.ebi.ac.uk/pdbsum/6eec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eec ProSAT]</span></td></tr>
 </table>
 == Function ==

6eec

From Proteopedia

Revision as of 00:24, 11 April 2020

Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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