6psu

From Proteopedia

(Difference between revisions)

Revision as of 07:02, 29 April 2020

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and rpsT P2 promoter

Structural highlights

6psu is a 10 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	traR, ECOK12F083 ("Bacillus coli" Migula 1895), rpoA, pez, phs, sez, b3295, JW3257 ("Bacillus coli" Migula 1895), rpoB, Z5560, ECs4910 ("Bacillus coli" Migula 1895), rpoC, tabB, b3988, JW3951 ("Bacillus coli" Migula 1895), rpoZ, Z5075, ECs4524 ("Bacillus coli" Migula 1895), rpoD ("Bacillus coli" Migula 1895)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q0P6L9_ECOLX] 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.[HAMAP-Rule:MF_00963][SAAS:SAAS00535554] [RPOB_ECO57] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [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] [RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [RPOZ_ECO57] 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 (By similarity).

Publication Abstract from PubMed

Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.

Stepwise Promoter Melting by Bacterial RNA Polymerase.,Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA Mol Cell. 2020 Mar 2. pii: S1097-2765(20)30110-6. doi:, 10.1016/j.molcel.2020.02.017. PMID:32160514^[1]

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

References

↑ Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA. Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol Cell. 2020 Mar 2. pii: S1097-2765(20)30110-6. doi:, 10.1016/j.molcel.2020.02.017. PMID:32160514 doi:http://dx.doi.org/10.1016/j.molcel.2020.02.017

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/6psu"

@@ Line 3: / Line 3: @@
 <StructureSection load='6psu' size='340' side='right'caption='[[6psu]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6psu]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PSU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6psu]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PSU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <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">traR, ECOK12F083 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6psu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psu OCA], [http://pdbe.org/6psu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6psu RCSB], [http://www.ebi.ac.uk/pdbsum/6psu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6psu ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6psu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psu OCA], [http://pdbe.org/6psu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6psu RCSB], [http://www.ebi.ac.uk/pdbsum/6psu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6psu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus coli migula 1895]]
 [[Category: DNA-directed RNA polymerase]]
 [[Category: Large Structures]]

6psu

From Proteopedia

Revision as of 07:02, 29 April 2020

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and rpsT P2 promoter

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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