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| | <StructureSection load='5d4d' size='340' side='right'caption='[[5d4d]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='5d4d' size='340' side='right'caption='[[5d4d]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5d4d]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2], [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D4D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D4D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5d4d]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus], [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D4D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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">[[4g7h|4g7h]], [[5d4e|5d4e]], [[5d4c|5d4c]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5d4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d4d OCA], [https://pdbe.org/5d4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d4d RCSB], [https://www.ebi.ac.uk/pdbsum/5d4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d4d ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sigA, rpoD, TT_C0164 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=5d4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d4d OCA], [http://pdbe.org/5d4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d4d RCSB], [http://www.ebi.ac.uk/pdbsum/5d4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d4d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] 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). [[http://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/SIGA_THET2 SIGA_THET2]] 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] | + | [https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed RNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Thermus thermophilus]] | | [[Category: Thermus thermophilus]] |
| - | [[Category: Thet2]] | + | [[Category: Thermus thermophilus HB27]] |
| - | [[Category: Thet8]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Ebright, R H]] | + | [[Category: Ebright RH]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Zhang Y]] |
| - | [[Category: Bacterial]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Dna-directed rna polymerase]]
| + | |
| - | [[Category: Gene expression regulation]]
| + | |
| - | [[Category: Genetic]]
| + | |
| - | [[Category: Ncin]]
| + | |
| - | [[Category: Non-canonical initiating nucleotide]]
| + | |
| - | [[Category: Primer-dependent initiation]]
| + | |
| - | [[Category: Promoter region]]
| + | |
| - | [[Category: Protein conformation]]
| + | |
| - | [[Category: Rna polymerase]]
| + | |
| - | [[Category: Sigma factor]]
| + | |
| - | [[Category: Single-stranded]]
| + | |
| - | [[Category: Transcription initiation]]
| + | |
| - | [[Category: Transcription-dna complex]]
| + | |
| Structural highlights
Function
RPOA_THET8 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Publication Abstract from PubMed
The chemical nature of the 5' end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency, and has been proposed to provide a layer of 'epitranscriptomic' gene regulation. Recently it has been shown that some bacterial RNA species carry a 5'-end structure reminiscent of the 5' 7-methylguanylate 'cap' in eukaryotic RNA. In particular, RNA species containing a 5'-end nicotinamide adenine dinucleotide (NAD+) or 3'-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated 'ab initio capping' may occur in all organisms.
The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA.,Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE Nature. 2016 Jul 21;535(7612):444-7. PMID:27383794[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE. The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA. Nature. 2016 Jul 21;535(7612):444-7. PMID:27383794 doi:http://dx.doi.org/10.1038/nature18622
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