This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6rin

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:27, 7 August 2019

Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex bound to GreB transcription factor

Structural highlights

6rin is a 9 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	6rh3, 6ri7, 6ri9
Gene:	greB, A6581_04870, A6592_17860, A9819_19355, ACN81_28045, AJ318_12850, AM446_03280, AM465_06470, AW059_21840, AW106_06800, AWP75_19390, B1K96_23455, B7C53_02740, B9M99_05190, B9N33_11850, B9T59_15180, BB545_11775, BE963_07880, BEN53_20780, BER14_23830, BIQ87_19125, BIU72_15205, BIZ41_07270, BN17_33411, BTQ04_09175, BTQ06_11100, BWP17_00335, BZL69_06140, C1I57_22680, C2M16_11315, C4K41_11925, C4M78_15275, C5715_11665, C5P43_01370, C5P44_10555, C6986_21785, C6B13_13810, C7B02_12915, C7B06_17550, C7B07_17730, C7B08_15410, CCZ14_09505, CCZ17_12365, CDL37_28230, CIJ94_13670, COD30_08990, COD46_24585, CQP61_02655, CR538_01935, CR539_22285, CRD98_08015, CRE06_04505, CRM83_22430, CRT43_20450, CRT46_19780, CSB64_14420, CT143_16930, CT146_14880, CVH05_26415, CWM24_10205, CXB56_05285, D1900_14635, D2183_13810, D2F89_07605, D3I61_20125, D5F38_05860, D6X47_11590, D7K63_10550, D7Y10_09590, D9D33_12115, D9D43_04330, D9E30_17490, D9E34_05680, D9E35_12335, D9E49_05660, D9F02_06885, D9F12_05730, D9F17_12145, D9F21_10030, D9G11_13190, D9G22_12525, D9G42_17600, D9G48_02635, D9G53_04685, D9H12_12450, D9H53_09445, D9H70_16165, D9H94_02685, D9I20_11335, D9I47_16295, D9I52_07930, D9I82_17890, D9I88_04675, D9J03_03135, D9J39_10095, D9J44_13380, D9J46_06810, D9K10_10415, DD762_12135, DIV22_04250, DL545_02535, DL800_24380, DL925_02870, DLU27_04270, DNQ45_10270, DNR41_15135, DNX30_18525, DOT75_01925, DP258_06460, DQE83_21230, DQF57_08805, DQP22_03685, DS732_24825, DS966_15260, DTL90_06605, DTM10_13330, DTM25_09000, DTM45_15925, DU309_12225, DU321_12435, DU333_19320, EA140_12925, EAI36_16755, EB510_07630, EB553_06270, EB569_05025, EB595_04935, ECs4248, ED060_02600, ED098_03500, ED124_04345, ED287_06925, ED600_01330, ED648_05650, ED653_03405, ED658_07555, ED944_05965, EEO96_14735, EEP03_05760, EF364_04490, EFV06_08470, EGT48_13510, EGY17_06960, EIA08_11750, EIA21_13775, HMPREF3040_00520 (ECOLI), rpoA, pez, phs, sez, b3295, JW3257 (ECOLI), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 (ECOLI), rpoC, tabB, b3988, JW3951 (ECOLI), rpoZ, b3649, JW3624 (ECOLI)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [C3SQ22_ECOLX] Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length.[HAMAP-Rule:MF_00930] [RPOZ_ECOLI] 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] [RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321]

Publication Abstract from PubMed

Regulatory sequences or erroneous incorporations during DNA transcription cause RNA polymerase backtracking and inactivation in all kingdoms of life. Reactivation requires RNA transcript cleavage. Essential transcription factors (GreA and GreB, or TFIIS) accelerate this reaction. We report four cryo-EM reconstructions of Escherichia coli RNA polymerase representing the entire reaction pathway: (1) a backtracked complex; a backtracked complex with GreB (2) before and (3) after RNA cleavage; and (4) a reactivated, substrate-bound complex with GreB before RNA extension. Compared with eukaryotes, the backtracked RNA adopts a different conformation. RNA polymerase conformational changes cause distinct GreB states: a fully engaged GreB before cleavage; a disengaged GreB after cleavage; and a dislodged, loosely bound GreB removed from the active site to allow RNA extension. These reconstructions provide insight into the catalytic mechanism and dynamics of RNA cleavage and extension and suggest how GreB targets backtracked complexes without interfering with canonical transcription.

Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation.,Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A Mol Cell. 2019 May 8. pii: S1097-2765(19)30321-1. doi:, 10.1016/j.molcel.2019.04.029. PMID:31103420^[1]

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

References

↑ Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A. Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation. Mol Cell. 2019 May 8. pii: S1097-2765(19)30321-1. doi:, 10.1016/j.molcel.2019.04.029. PMID:31103420 doi:http://dx.doi.org/10.1016/j.molcel.2019.04.029

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/6rin"

@@ Line 3: / Line 3: @@
 <StructureSection load='6rin' size='340' side='right'caption='[[6rin]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6rin]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RIN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6rin]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RIN 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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6rh3|6rh3]], [[6ri7|6ri7]], [[6ri9|6ri9]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">greB, A6581_04870, A6592_17860, A9819_19355, ACN81_28045, AJ318_12850, AM446_03280, AM465_06470, AW059_21840, AW106_06800, AWP75_19390, B1K96_23455, B7C53_02740, B9M99_05190, B9N33_11850, B9T59_15180, BB545_11775, BE963_07880, BEN53_20780, BER14_23830, BIQ87_19125, BIU72_15205, BIZ41_07270, BN17_33411, BTQ04_09175, BTQ06_11100, BWP17_00335, BZL69_06140, C1I57_22680, C2M16_11315, C4K41_11925, C4M78_15275, C5715_11665, C5P43_01370, C5P44_10555, C6986_21785, C6B13_13810, C7B02_12915, C7B06_17550, C7B07_17730, C7B08_15410, CCZ14_09505, CCZ17_12365, CDL37_28230, CIJ94_13670, COD30_08990, COD46_24585, CQP61_02655, CR538_01935, CR539_22285, CRD98_08015, CRE06_04505, CRM83_22430, CRT43_20450, CRT46_19780, CSB64_14420, CT143_16930, CT146_14880, CVH05_26415, CWM24_10205, CXB56_05285, D1900_14635, D2183_13810, D2F89_07605, D3I61_20125, D5F38_05860, D6X47_11590, D7K63_10550, D7Y10_09590, D9D33_12115, D9D43_04330, D9E30_17490, D9E34_05680, D9E35_12335, D9E49_05660, D9F02_06885, D9F12_05730, D9F17_12145, D9F21_10030, D9G11_13190, D9G22_12525, D9G42_17600, D9G48_02635, D9G53_04685, D9H12_12450, D9H53_09445, D9H70_16165, D9H94_02685, D9I20_11335, D9I47_16295, D9I52_07930, D9I82_17890, D9I88_04675, D9J03_03135, D9J39_10095, D9J44_13380, D9J46_06810, D9K10_10415, DD762_12135, DIV22_04250, DL545_02535, DL800_24380, DL925_02870, DLU27_04270, DNQ45_10270, DNR41_15135, DNX30_18525, DOT75_01925, DP258_06460, DQE83_21230, DQF57_08805, DQP22_03685, DS732_24825, DS966_15260, DTL90_06605, DTM10_13330, DTM25_09000, DTM45_15925, DU309_12225, DU321_12435, DU333_19320, EA140_12925, EAI36_16755, EB510_07630, EB553_06270, EB569_05025, EB595_04935, ECs4248, ED060_02600, ED098_03500, ED124_04345, ED287_06925, ED600_01330, ED648_05650, ED653_03405, ED658_07555, ED944_05965, EEO96_14735, EEP03_05760, EF364_04490, EFV06_08470, EGT48_13510, EGY17_06960, EIA08_11750, EIA21_13775, HMPREF3040_00520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6rin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rin OCA], [http://pdbe.org/6rin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rin RCSB], [http://www.ebi.ac.uk/pdbsum/6rin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rin ProSAT]</span></td></tr>
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Ecoli]]
 [[Category: Large Structures]]
 [[Category: Abdelkareem, M]]

6rin

From Proteopedia

Revision as of 06:27, 7 August 2019

Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex bound to GreB transcription factor

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox