5ipm

From Proteopedia

(Difference between revisions)

Revision as of 07:27, 3 June 2020

SigmaS-transcription initiation complex with 4-nt nascent RNA

Structural highlights

5ipm is a 9 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:	,
NonStd Res:
Related:	5ipl, 5ipn
Gene:	rpoA, pez, phs, sez, b3295, JW3257 ("Bacillus coli" Migula 1895), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ("Bacillus coli" Migula 1895), rpoC, tabB, b3988, JW3951 ("Bacillus coli" Migula 1895), rpoZ, b3649, JW3624 ("Bacillus coli" Migula 1895), rpoS, appR, katF, nur, otsX, sigS, b2741, JW5437 ("Bacillus coli" Migula 1895)
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] [RPOS_ECOLI] 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 master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.[HAMAP-Rule:MF_00959]^[1] ^[2] ^[3] ^[4] ^[5] Protects stationary phase cells from killing induced by endoribonuclease MazF.^[6]

Publication Abstract from PubMed

In bacteria, multiple sigma factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the sigma factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures ofEcolitranscription initiation complexes (TICs) containing the stress-responsive sigmaSfactor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (sigmaS-TIC) at about 3.9-A resolution. The structures show the 3D topology of the sigmaSfactor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, sigmaS-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these sigmaS-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.

Structures of E. coli sigmaS-transcription initiation complexes provide new insights into polymerase mechanism.,Liu B, Zuo Y, Steitz TA Proc Natl Acad Sci U S A. 2016 Mar 28. pii: 201520555. PMID:27035955^[7]

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

References

↑ Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics. 2004 Dec;272(5):580-91. Epub 2004 Nov 19. PMID:15558318 doi:http://dx.doi.org/10.1007/s00438-004-1089-2
↑ Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol. 2005 Mar;187(5):1591-603. PMID:15716429 doi:http://dx.doi.org/10.1128/JB.187.5.1591-1603.2005
↑ Rahman M, Hasan MR, Oba T, Shimizu K. Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations. Biotechnol Bioeng. 2006 Jun 20;94(3):585-95. PMID:16511888 doi:http://dx.doi.org/10.1002/bit.20858
↑ Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P. In vitro transcription profiling of the sigmaS subunit of bacterial RNA polymerase: re-definition of the sigmaS regulon and identification of sigmaS-specific promoter sequence elements. Nucleic Acids Res. 2011 Jul;39(13):5338-55. doi: 10.1093/nar/gkr129. Epub 2011, Mar 11. PMID:21398637 doi:http://dx.doi.org/10.1093/nar/gkr129
↑ Tanaka K, Takayanagi Y, Fujita N, Ishihama A, Takahashi H. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3511-5. PMID:8475100
↑ Kolodkin-Gal I, Engelberg-Kulka H. The stationary-phase sigma factor sigma(S) is responsible for the resistance of Escherichia coli stationary-phase cells to mazEF-mediated cell death. J Bacteriol. 2009 May;191(9):3177-82. doi: 10.1128/JB.00011-09. Epub 2009 Feb 27. PMID:19251848 doi:http://dx.doi.org/10.1128/JB.00011-09
↑ Liu B, Zuo Y, Steitz TA. Structures of E. coli sigmaS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A. 2016 Mar 28. pii: 201520555. PMID:27035955 doi:http://dx.doi.org/10.1073/pnas.1520555113

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/5ipm"

@@ Line 1: / Line 1: @@
 ==SigmaS-transcription initiation complex with 4-nt nascent RNA==
-<StructureSection load='5ipm' size='340' side='right' caption='[[5ipm]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
+<StructureSection load='5ipm' size='340' side='right'caption='[[5ipm]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ipm]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ipm]] is a 9 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=5IPM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IPM 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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ipl|5ipl]], [[5ipn|5ipn]]</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=562 "Bacillus coli" Migula 1895]), 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=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, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoS, appR, katF, nur, otsX, sigS, b2741, JW5437 ([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=5ipm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipm OCA], [http://pdbe.org/5ipm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipm RCSB], [http://www.ebi.ac.uk/pdbsum/5ipm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipm 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=5ipm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipm OCA], [http://pdbe.org/5ipm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipm RCSB], [http://www.ebi.ac.uk/pdbsum/5ipm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipm ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 22: @@
 </div>
 <div class="pdbe-citations 5ipm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Bacillus coli migula 1895]]
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Liu, B]]
 [[Category: Steitz, T A]]

5ipm

From Proteopedia

Revision as of 07:27, 3 June 2020

SigmaS-transcription initiation complex with 4-nt nascent RNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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