6tyf

From Proteopedia

(Difference between revisions)

Revision as of 10:45, 27 March 2020

Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer

Structural highlights

6tyf is a 9 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.
Gene:	rpoA ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoB ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoC, rpoC_1, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860, EUB11_05575, SAMEA2682835_07420, SAMEA2682864_01702 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_03677, ERS024213_01369, ERS024276_01577, ERS027644_00478, ERS027646_01439, ERS027651_03169, ERS027653_00843, ERS027659_01429, ERS027661_02200, ERS027666_04715, ERS031537_03443, EU767_08910, EU768_15085, EU769_05250, EU770_14555, EU771_05130, EU773_14340, EU774_06465, EU775_07590, EU776_17830, EU777_06800, EUB02_12495, EUB03_09550, EUB06_03645, EUB07_12165, EUB08_05285, EUB09_00425, EUB10_04215, EUB11_10790, EUB13_01060, EUB14_01055, EUB16_00425, SAMEA2682864_01599, SAMEA2683035_01133 ("Bacillus tuberculosis" (Zopf 1883) Klein 1884), sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ERS024213_03781, ERS027644_01708, ERS027646_03649, ERS027651_00554, ERS027654_02031, ERS027659_03608, ERS027661_02428, ERS027666_03497, ERS031537_01383, ERS124361_02832, EU767_20440, EU768_17405, EU769_19535, EU770_10565, EU771_18640, EU773_15915, EU774_01235, EU775_01235, EU776_08285, EU777_18775, EUB02_13395, EUB03_01225, EUB07_01225, EUB08_01615, EUB09_12390, EUB10_16580, EUB11_05940, EUB12_18145, EUB13_14065, EUB14_03980, EUB16_03020, SAMEA2682835_06130, SAMEA2682864_01771, SAMEA2683035_02456 ("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

[A0A045J9E2_MYCTX] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279][SAAS:SAAS00365746] [RPOB_MYCTO] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOA_MYCTA] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [A0A045H2R3_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:SAAS00387808]

Publication Abstract from PubMed

All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "sigma-finger" of the bacterial transcription initiation factor sigma. The structures reveal that-for both the primary sigma-factor and extracytoplasmic (ECF) sigma-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "sigma-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from approximately 5 nt to approximately 10 nt.

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.,Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y Proc Natl Acad Sci U S A. 2020 Mar 3. pii: 1920747117. doi:, 10.1073/pnas.1920747117. PMID:32127479^[1]

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

References

↑ Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y. RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Proc Natl Acad Sci U S A. 2020 Mar 3. pii: 1920747117. doi:, 10.1073/pnas.1920747117. PMID:32127479 doi:http://dx.doi.org/10.1073/pnas.1920747117

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/6tyf"

@@ Line 3: / Line 3: @@
 <StructureSection load='6tyf' size='340' side='right'caption='[[6tyf]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6tyf]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TYF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6tyf]] is a 9 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=6TYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TYF FirstGlance]. <br>
-</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>
+</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 ([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, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860, EUB11_05575, SAMEA2682835_07420, 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, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_03677, ERS024213_01369, ERS024276_01577, ERS027644_00478, ERS027646_01439, ERS027651_03169, ERS027653_00843, ERS027659_01429, ERS027661_02200, ERS027666_04715, ERS031537_03443, EU767_08910, EU768_15085, EU769_05250, EU770_14555, EU771_05130, EU773_14340, EU774_06465, EU775_07590, EU776_17830, EU777_06800, EUB02_12495, EUB03_09550, EUB06_03645, EUB07_12165, EUB08_05285, EUB09_00425, EUB10_04215, EUB11_10790, EUB13_01060, EUB14_01055, EUB16_00425, SAMEA2682864_01599, SAMEA2683035_01133 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ERS024213_03781, ERS027644_01708, ERS027646_03649, ERS027651_00554, ERS027654_02031, ERS027659_03608, ERS027661_02428, ERS027666_03497, ERS031537_01383, ERS124361_02832, EU767_20440, EU768_17405, EU769_19535, EU770_10565, EU771_18640, EU773_15915, EU774_01235, EU775_01235, EU776_08285, EU777_18775, EUB02_13395, EUB03_01225, EUB07_01225, EUB08_01615, EUB09_12390, EUB10_16580, EUB11_05940, EUB12_18145, EUB13_14065, EUB14_03980, EUB16_03020, SAMEA2682835_06130, SAMEA2682864_01771, SAMEA2683035_02456 ([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=6tyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyf OCA], [http://pdbe.org/6tyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tyf RCSB], [http://www.ebi.ac.uk/pdbsum/6tyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyf ProSAT]</span></td></tr>
 </table>

6tyf

From Proteopedia

Revision as of 10:45, 27 March 2020

Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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