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.

5nsr

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 16:46, 11 December 2019

Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex

Structural highlights

5nsr is a 8 chain structure with sequence from [1], "bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886 and Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:	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), rpoN, SAMEA3531867_02981 ("Bacillus pneumoniae" (Schroeter 1886) Flugge 1886)
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] [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [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] [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] [A0A0J4U551_KLEPN] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774]

Publication Abstract from PubMed

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative sigma54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 A. Our structures show how RNAP-sigma54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and sigma54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.,Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X Mol Cell. 2017 Jul 6;67(1):106-116.e4. doi: 10.1016/j.molcel.2017.05.010. Epub, 2017 Jun 1. PMID:28579332^[1]

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

References

↑ Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X. Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol Cell. 2017 Jul 6;67(1):106-116.e4. doi: 10.1016/j.molcel.2017.05.010. Epub, 2017 Jun 1. PMID:28579332 doi:http://dx.doi.org/10.1016/j.molcel.2017.05.010

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/5nsr"

@@ Line 1: / Line 1: @@
 ==Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex==
-<StructureSection load='5nsr' size='340' side='right' caption='[[5nsr]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
+<StructureSection load='5nsr' size='340' side='right'caption='[[5nsr]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nsr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NSR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nsr]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NSR FirstGlance]. <br>
 </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">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]), rpoN, SAMEA3531867_02981 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=5nsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nsr OCA], [http://pdbe.org/5nsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nsr RCSB], [http://www.ebi.ac.uk/pdbsum/5nsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nsr ProSAT]</span></td></tr>
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5nsr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RNA polymerase|RNA polymerase]]
+*[[Sigma factor|Sigma factor]]
 == References ==
 <references/>
@@ Line 24: / Line 29: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Buck, M]]
 [[Category: Darbari, V C]]

5nsr

From Proteopedia

Revision as of 16:46, 11 December 2019

Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox