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| | <StructureSection load='4mex' size='340' side='right'caption='[[4mex]], [[Resolution|resolution]] 3.90Å' scene=''> | | <StructureSection load='4mex' size='340' side='right'caption='[[4mex]], [[Resolution|resolution]] 3.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mex]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MEX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mex]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MEX 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=28H:(2R,3R)-3-HYDROXY-2,4-DIMETHYLPENTANOIC+ACID'>28H</scene>, <scene name='pdbligand=28J:D-ALLOISOLEUCINE'>28J</scene>, <scene name='pdbligand=28K:(2E)-3-{(2S)-2-[(1R)-1-HYDROXYETHYL]OXIRAN-2-YL}PROP-2-ENOIC+ACID'>28K</scene>, <scene name='pdbligand=2TL:D-ALLOTHREONINE'>2TL</scene>, <scene name='pdbligand=D4P:(2S)-AMINO(4-HYDROXYPHENYL)ACETIC+ACID'>D4P</scene>, <scene name='pdbligand=MEA:N-METHYLPHENYLALANINE'>MEA</scene>, <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=28H:(2R,3R)-3-HYDROXY-2,4-DIMETHYLPENTANOIC+ACID'>28H</scene>, <scene name='pdbligand=28J:D-ALLOISOLEUCINE'>28J</scene>, <scene name='pdbligand=28K:(2E)-3-{(2S)-2-[(1R)-1-HYDROXYETHYL]OXIRAN-2-YL}PROP-2-ENOIC+ACID'>28K</scene>, <scene name='pdbligand=2TL:D-ALLOTHREONINE'>2TL</scene>, <scene name='pdbligand=D4P:(2S)-AMINO(4-HYDROXYPHENYL)ACETIC+ACID'>D4P</scene>, <scene name='pdbligand=MEA:N-METHYLPHENYLALANINE'>MEA</scene></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=4mex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mex OCA], [https://pdbe.org/4mex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mex RCSB], [https://www.ebi.ac.uk/pdbsum/4mex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mex ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mey|4mey]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3295, BN17_32291, ECs4160, JW3257, LF82_1958, pez, phs, rpoA, sez ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b3987, groN, JW3950, K758_06833, nitB, rif, ron, rpoB, stl, stv, tabD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b3988, BN17_39521, ECs4911, JW3951, LF82_1960, rpoC, tabB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b3649, BN17_35921, ECs4524, JW3624, LF82_1966, rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), alt, b3067, JW3039, rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4mex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mex OCA], [http://pdbe.org/4mex PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mex RCSB], [http://www.ebi.ac.uk/pdbsum/4mex PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mex ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/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/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/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium. | + | [https://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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==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 == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ecoli]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Arnold, E]] | + | [[Category: Streptomyces sp]] |
| - | [[Category: Ebright, R H]] | + | [[Category: Arnold E]] |
| - | [[Category: Feng, Y]] | + | [[Category: Ebright RH]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Feng Y]] |
| - | [[Category: Dna binding]] | + | [[Category: Zhang Y]] |
| - | [[Category: Rna polymerase]]
| + | |
| - | [[Category: Transferase-antibiotic complex]]
| + | |
| Structural highlights
4mex is a 14 chain structure with sequence from Escherichia coli K-12 and Streptomyces sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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]
Publication Abstract from PubMed
We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap' comprising the 'bridge-helix N-terminal hinge', 'F-loop', and 'link region'. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.DOI: http://dx.doi.org/10.7554/eLife.02451.001.
Transcription inhibition by the depsipeptide antibiotic salinamide A.,Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH Elife. 2014 Apr 30;3:e02451. doi: 10.7554/eLife.02451. PMID:24843001[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. Transcription inhibition by the depsipeptide antibiotic salinamide A. Elife. 2014 Apr 30;3:e02451. doi: 10.7554/eLife.02451. PMID:24843001 doi:http://dx.doi.org/10.7554/eLife.02451
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