|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of Thermus thermophilus transcription initiation complex== | | ==Crystal structure of Thermus thermophilus transcription initiation complex== |
| - | <StructureSection load='4g7h' size='340' side='right' caption='[[4g7h]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='4g7h' size='340' side='right'caption='[[4g7h]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4g7h]] is a 16 chain structure with sequence from [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=4G7H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G7H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4g7h]] is a 16 chain structure with sequence from [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=4G7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G7H 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g7o|4g7o]], [[4g7z|4g7z]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoD, TTHA0532 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=4g7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g7h OCA], [https://pdbe.org/4g7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g7h RCSB], [https://www.ebi.ac.uk/pdbsum/4g7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g7h ProSAT]</span></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=4g7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g7h OCA], [http://pdbe.org/4g7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g7h RCSB], [http://www.ebi.ac.uk/pdbsum/4g7h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g7h 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_THET8 RPOA_THET8]] 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/Q5SKW1_THET8 Q5SKW1_THET8]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715] 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 (By similarity).[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;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 A resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, sigma(A), and a promoter DNA fragment corresponding to the transcription bubble and downstream dsDNA of the RNAP-promoter open complex. The structures show that sigma recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases, and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between sigma and template-strand ssDNA preorganize template-strand ssDNA to engage the RNAP active center.
| + | |
| - | | + | |
| - | Structural Basis of Transcription Initiation.,Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH Science. 2012 Oct 18. PMID:23086998<ref>PMID:23086998</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 4g7h" style="background-color:#fffaf0;"></div>
| + | |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| - | *[[Sigma factor|Sigma factor]] | + | *[[Sigma factor 3D structures|Sigma factor 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Thermus thermophilus]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Thet8]]
| + | [[Category: Ebright RH]] |
| - | [[Category: Ebright, R H]] | + | [[Category: Zhang Y]] |
| - | [[Category: Zhang, Y]] | + | |
| - | [[Category: Nucleoid]]
| + | |
| - | [[Category: Open complex]]
| + | |
| - | [[Category: Promoter dna]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Rna polymerase]]
| + | |
| - | [[Category: Rnap-promoter complex]]
| + | |
| - | [[Category: Rnap-promoter open complex]]
| + | |
| - | [[Category: Rpo]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription initiation]]
| + | |
| - | [[Category: Transcription initiation complex]]
| + | |
| - | [[Category: Transcription initiation factor sigma some]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
