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6c05

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Revision as of 09:28, 18 December 2019

Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state

Structural highlights

6c05 is a 7 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, rpoA_1, CLD25_18970, ERS007661_01801, ERS007663_01917, ERS007665_01054, ERS007670_00938, ERS007672_03180, ERS007679_01858, ERS007688_02121, ERS007703_04392, ERS007720_00529, ERS007722_04215, ERS023446_02770, ERS024213_02470, ERS027644_00781, ERS027646_02177, ERS027652_00409, ERS027653_00362, ERS027654_02191, ERS027656_00886, ERS027659_01235, ERS027661_02549, ERS027666_01143, ERS124361_03550, SAMEA2682864_03600, SAMEA2683035_02863 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoB, SAMEA2682864_01701 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoC, rpoC_1, CLD25_03785, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, SAMEA2682864_01702 ("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, hrdB_2, CLD25_14885, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS023446_01203, ERS024213_00371, ERS024276_00878, ERS027644_01437, ERS027646_01351, ERS027653_01295, ERS027661_00252, ERS124361_02215, SAMEA2682864_02073, SAMEA2683035_01696 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rbpA, CLD25_11245, ERS007670_01223, ERS007672_02518, ERS007679_02287, ERS007681_03389, ERS007688_02707, ERS007703_03544, ERS007720_03893, ERS007722_02881, ERS007731_02971, ERS007739_00749, ERS007741_03837, ERS023446_04025, ERS024213_00234, ERS024276_03708, ERS027644_04191, ERS027646_02841, ERS027652_02278, ERS027653_01824, ERS027654_04301, ERS027656_03007, ERS027659_00863, ERS027661_00907, ERS027666_04473, ERS031537_02569, ERS124361_01290, SAMEA2682864_00634, SAMEA2683035_00392 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[A0A045IP01_MYCTX] Binds to RNA polymerase (RNAP), stimulating transcription from principal, but not alternative sigma factor promoters.[HAMAP-Rule:MF_01483] [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] [A0A045J8T1_MYCTX] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059] [A0A045J9E2_MYCTX] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279][SAAS:SAAS00365746] [V9Z879_MYCTX] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [A0A045HD00_MYCTX] 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.[SAAS:SAAS00535554]

Publication Abstract from PubMed

Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 A cryo-electron microscopy structure of a complete M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis. Additional structures define conformational states of M. tuberculosis RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket.

Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts.,Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA Elife. 2018 Feb 26;7. pii: 34823. doi: 10.7554/eLife.34823. PMID:29480804^[1]

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

References

↑ Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. Elife. 2018 Feb 26;7. pii: 34823. doi: 10.7554/eLife.34823. PMID:29480804 doi:http://dx.doi.org/10.7554/eLife.34823

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/6c05"

@@ Line 1: / Line 1: @@
 ==Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state==
-<StructureSection load='6c05' size='340' side='right' caption='[[6c05]], [[Resolution|resolution]] 5.15&Aring;' scene=''>
+<StructureSection load='6c05' size='340' side='right'caption='[[6c05]], [[Resolution|resolution]] 5.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6c05]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C05 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C05 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6c05]] is a 7 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=6C05 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C05 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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, rpoA_1, CLD25_18970, ERS007661_01801, ERS007663_01917, ERS007665_01054, ERS007670_00938, ERS007672_03180, ERS007679_01858, ERS007688_02121, ERS007703_04392, ERS007720_00529, ERS007722_04215, ERS023446_02770, ERS024213_02470, ERS027644_00781, ERS027646_02177, ERS027652_00409, ERS027653_00362, ERS027654_02191, ERS027656_00886, ERS027659_01235, ERS027661_02549, ERS027666_01143, ERS124361_03550, SAMEA2682864_03600, SAMEA2683035_02863 ([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, rpoC_1, CLD25_03785, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, SAMEA2682864_01702 ([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, hrdB_2, CLD25_14885, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS023446_01203, ERS024213_00371, ERS024276_00878, ERS027644_01437, ERS027646_01351, ERS027653_01295, ERS027661_00252, ERS124361_02215, SAMEA2682864_02073, SAMEA2683035_01696 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rbpA, CLD25_11245, ERS007670_01223, ERS007672_02518, ERS007679_02287, ERS007681_03389, ERS007688_02707, ERS007703_03544, ERS007720_03893, ERS007722_02881, ERS007731_02971, ERS007739_00749, ERS007741_03837, ERS023446_04025, ERS024213_00234, ERS024276_03708, ERS027644_04191, ERS027646_02841, ERS027652_02278, ERS027653_01824, ERS027654_04301, ERS027656_03007, ERS027659_00863, ERS027661_00907, ERS027666_04473, ERS031537_02569, ERS124361_01290, SAMEA2682864_00634, SAMEA2683035_00392 ([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=6c05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c05 OCA], [http://pdbe.org/6c05 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c05 RCSB], [http://www.ebi.ac.uk/pdbsum/6c05 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c05 ProSAT]</span></td></tr>
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 6c05" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Sigma factor|Sigma factor]]
 == References ==
 <references/>
@@ Line 24: / Line 28: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Campbell, E A]]
 [[Category: Chen, J]]

6c05

From Proteopedia

Revision as of 09:28, 18 December 2019

Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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