6eyd

From Proteopedia

(Difference between revisions)

Current revision

Structure of Mycobacterium smegmatis RNA polymerase Sigma-A holoenzyme

6eyd, resolution 4.20Å

Structural highlights

6eyd is a 6 chain structure with sequence from Mycs2. This structure supersedes the now removed PDB entry 6fed. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	rpoA, MSMEG_1524, MSMEI_1488 (MYCS2), rpoB, MSMEG_1367, MSMEI_1328 (MYCS2), rpoC, MSMEG_1368, MSMEI_1329 (MYCS2), rpoZ, MSMEG_3053, MSMEI_2977 (MYCS2), sigA, MSMEG_2758 (MYCS2)
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

[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]^[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] [RPOC_MYCS2] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]^[3] [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]^[4] [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]

Publication Abstract from PubMed

Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two so far unreported forms of Mycobacteium smegmatis RNAP: core, and holoenzyme containing sigma(A) but no other factors. Each form was detected by cryo-EM in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme, and confirm that region 1.1 of sigma(A) is directed into the primary channel of RNAP. Taken together, the presented study illuminates the conformational changes of unrestrained mycobacterial RNAP.IMPORTANCE We describe here 3D structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-EM. These structures fill the so far empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.

The Core and Holoenzyme forms of RNA Polymerase from Mycobacterium smegmatis.,Kouba T, Pospisil J, Hnilicova J, Sanderova H, Barvik I, Krasny L J Bacteriol. 2018 Nov 26. pii: JB.00583-18. doi: 10.1128/JB.00583-18. PMID:30478083^[5]

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. 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
↑ Kouba T, Pospisil J, Hnilicova J, Sanderova H, Barvik I, Krasny L. The Core and Holoenzyme forms of RNA Polymerase from Mycobacterium smegmatis. J Bacteriol. 2018 Nov 26. pii: JB.00583-18. doi: 10.1128/JB.00583-18. PMID:30478083 doi:http://dx.doi.org/10.1128/JB.00583-18

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/6eyd"

@@ Line 3: / Line 3: @@
 <SX load='6eyd' size='340' side='right' viewer='molstar' caption='[[6eyd]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6eyd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EYD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6EYD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6eyd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6fed 6fed]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EYD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6EYD FirstGlance]. <br>
 </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">rpoA, MSMEG_1524, MSMEI_1488 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoB, MSMEG_1367, MSMEI_1328 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoC, MSMEG_1368, MSMEI_1329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoZ, MSMEG_3053, MSMEI_2977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), sigA, MSMEG_2758 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>

6eyd

From Proteopedia

Current revision

Structure of Mycobacterium smegmatis RNA polymerase Sigma-A holoenzyme

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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