5nss

From Proteopedia

(Difference between revisions)

Revision as of 06:32, 24 October 2018

Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex

Structural highlights

5nss is a 14 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), pspF, ycjB, b1303, JW1296 (ECOLI), SAMEA4362693_02699, SM87_03359 ("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

[A0A060VKE4_KLEPN] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774] [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] [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_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] [PSPF_ECOLI] Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.^[1] ^[2] ^[3]

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^[4]

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

References

↑ Jovanovic G, Weiner L, Model P. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J Bacteriol. 1996 Apr;178(7):1936-45. PMID:8606168
↑ Lloyd LJ, Jones SE, Jovanovic G, Gyaneshwar P, Rolfe MD, Thompson A, Hinton JC, Buck M. Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG). J Biol Chem. 2004 Dec 31;279(53):55707-14. Epub 2004 Oct 13. PMID:15485810 doi:10.1074/jbc.M408994200
↑ Joly N, Burrows PC, Engl C, Jovanovic G, Buck M. A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation. J Mol Biol. 2009 Dec 11;394(4):764-75. doi: 10.1016/j.jmb.2009.09.055. Epub 2009 , Oct 3. PMID:19804784 doi:10.1016/j.jmb.2009.09.055
↑ 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/5nss"

@@ Line 3: / Line 3: @@
 <StructureSection load='5nss' size='340' side='right' caption='[[5nss]], [[Resolution|resolution]] 5.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nss]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NSS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nss]] is a 14 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=5NSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NSS 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]), pspF, ycjB, b1303, JW1296 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), SAMEA4362693_02699, SM87_03359 ([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=5nss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nss OCA], [http://pdbe.org/5nss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nss RCSB], [http://www.ebi.ac.uk/pdbsum/5nss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nss ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/A0A060VKE4_KLEPN A0A060VKE4_KLEPN]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOZ_ECOLI 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] [[http://www.uniprot.org/uniprot/RPOA_ECOLI 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] [[http://www.uniprot.org/uniprot/PSPF_ECOLI PSPF_ECOLI]] Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.<ref>PMID:8606168</ref> <ref>PMID:15485810</ref> <ref>PMID:19804784</ref>
+[[http://www.uniprot.org/uniprot/A0A060VKE4_KLEPN A0A060VKE4_KLEPN]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOA_ECOLI 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] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOZ_ECOLI 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] [[http://www.uniprot.org/uniprot/PSPF_ECOLI PSPF_ECOLI]] Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.<ref>PMID:8606168</ref> <ref>PMID:15485810</ref> <ref>PMID:19804784</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5nss" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RNA polymerase|RNA polymerase]]
+*[[Sigma factor|Sigma factor]]
+*[[Transcriptional activator|Transcriptional activator]]
 == References ==
 <references/>
@@ Line 24: / Line 30: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Ecoli]]
 [[Category: Buck, M]]
 [[Category: Darbari, V C]]

5nss

From Proteopedia

Revision as of 06:32, 24 October 2018

Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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