5tw1

From Proteopedia

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Revision as of 19:21, 15 November 2017

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with RbpA

Structural highlights

5tw1 is a 11 chain structure with sequence from Mycs2 and Mycobacterium smegmatis str. mc2 155. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
NonStd Res:
Gene:	rbpA, MSMEG_3858, MSMEI_3768 (MYCS2), rpoD, sigA, MSMEG_2758, MSMEI_2690 (MYCS2)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[A0QW02_MYCS2] 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] [RPOB_MYCS2] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit often mutates to generate rifampicin (Rif) resistance. Interaction with RbpA partially restores Rif-inhibited transcription; once the subunit is Rif-resistant however RbpA no longer stimulates transcription.[HAMAP-Rule:MF_01321]^[1] [RPOA_MYCS2] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]^[2] [RBPA_MYCS2] Binds to RNA polymerase (RNAP), probably stimulating transcriptions from principal, but not alternative sigma factor promoters (By similarity). Partially restores transcription in the presence of rifampicin (Rif) in vitro; overexpression leads to an increase in the Rif tolerance in vivo, with smaller colonies. Seems to act by removing Rif from its binding site and preventing its further binding. No longer stimulates transcription in Rif-resistant RNA polymerase (with mutations in rpoB).^[3] ^[4] [RPOC_MYCS2] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]^[5] [RPOZ_MYCS2] 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]^[6]

Publication Abstract from PubMed

RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish thatRbpA and CarD cooperatively stimulate formation of anintermediate (RP2) leading to RPo; formation of RP2 islikely a bottleneck step at the majority of mycobacterial promoters. Once RPo forms, CarD also disfavors its isomerization back to RP2.We determined a 2.76 A-resolution crystal structure of a mycobacterial transcription initiation complex (TIC) with RbpA as well as a CarD/RbpA/TIC model. Both CarD and RbpA bind near the upstream edge of the -10 element where they likely facilitate DNA bending and impede transcription bubble collapse. In vivo studies demonstrate the essential role of RbpA, effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. This work provides a framework to understand the control of mycobacterial transcriptionby RbpA and CarD.

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA.,Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA Elife. 2017 Jan 9;6. pii: e22520. doi: 10.7554/eLife.22520. PMID:28067618^[7]

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

References

↑ Dey A, Verma AK, Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010 Mar;156(Pt 3):873-83. doi: 10.1099/mic.0.033670-0. Epub 2009, Nov 19. PMID:19926651 doi:http://dx.doi.org/10.1099/mic.0.033670-0
↑ Dey A, Verma AK, Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010 Mar;156(Pt 3):873-83. doi: 10.1099/mic.0.033670-0. Epub 2009, Nov 19. PMID:19926651 doi:http://dx.doi.org/10.1099/mic.0.033670-0
↑ Dey A, Verma AK, Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010 Mar;156(Pt 3):873-83. doi: 10.1099/mic.0.033670-0. Epub 2009, Nov 19. PMID:19926651 doi:http://dx.doi.org/10.1099/mic.0.033670-0
↑ Dey A, Verma AK, Chatterji D. Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA. Microbiology. 2011 Jul;157(Pt 7):2056-71. doi: 10.1099/mic.0.047480-0. Epub 2011 , Mar 17. PMID:21415119 doi:http://dx.doi.org/10.1099/mic.0.047480-0
↑ Dey A, Verma AK, Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010 Mar;156(Pt 3):873-83. doi: 10.1099/mic.0.033670-0. Epub 2009, Nov 19. PMID:19926651 doi:http://dx.doi.org/10.1099/mic.0.033670-0
↑ Dey A, Verma AK, Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010 Mar;156(Pt 3):873-83. doi: 10.1099/mic.0.033670-0. Epub 2009, Nov 19. PMID:19926651 doi:http://dx.doi.org/10.1099/mic.0.033670-0
↑ Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA. Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. Elife. 2017 Jan 9;6. pii: e22520. doi: 10.7554/eLife.22520. PMID:28067618 doi:http://dx.doi.org/10.7554/eLife.22520

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5tw1"

@@ Line 3: / Line 3: @@
 <StructureSection load='5tw1' size='340' side='right' caption='[[5tw1]], [[Resolution|resolution]] 2.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5tw1]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_(strain_atcc_700084_/_mc(2)155) Mycobacterium smegmatis (strain atcc 700084 / mc(2)155)] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TW1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5tw1]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TW1 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rbpA, MSMEG_3858, MSMEI_3768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoD, sigA, MSMEG_2758, MSMEI_2690 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=5tw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tw1 OCA], [http://pdbe.org/5tw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tw1 RCSB], [http://www.ebi.ac.uk/pdbsum/5tw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tw1 ProSAT]</span></td></tr>
@@ Line 26: / Line 27: @@
 [[Category: DNA-directed RNA polymerase]]
 [[Category: Mycobacterium smegmatis str. mc2 155]]
+[[Category: Mycs2]]
 [[Category: Campbell, E A]]
 [[Category: Darst, S A]]
 [[Category: Hubin, E A]]
 [[Category: Transcription activator-transferase-dna complex]]

5tw1

From Proteopedia

Revision as of 19:21, 15 November 2017

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with RbpA

Structural highlights

Function

Publication Abstract from PubMed

References

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