3dxj

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{{Seed}}
 
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[[Image:3dxj.png|left|200px]]
 
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==Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin==
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The line below this paragraph, containing "STRUCTURE_3dxj", creates the "Structure Box" on the page.
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<StructureSection load='3dxj' size='340' side='right'caption='[[3dxj]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3dxj]] is a 12 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=3DXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DXJ FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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<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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NE6:METHYL+[(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-DIMETHYLOCTA-2,4-DIENOYL]-2,4-DIOXO-3,4-DIHYDRO-2H-PYRAN-6-YL}HEXYLIDENE]CARBAMATE'>NE6</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3dxj| PDB=3dxj | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dxj OCA], [https://pdbe.org/3dxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dxj RCSB], [https://www.ebi.ac.uk/pdbsum/3dxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dxj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dx/3dxj_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dxj ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.
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===Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin===
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The RNA polymerase "switch region" is a target for inhibitors.,Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH Cell. 2008 Oct 17;135(2):295-307. PMID:18957204<ref>PMID:18957204</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3dxj" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18957204}}, adds the Publication Abstract to the page
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18957204 is the PubMed ID number.
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_18957204}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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3DXJ is a [[Protein complex]] structure of sequences from [http://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=3DXJ OCA].
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[[Category: Large Structures]]
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[[Category: Thermus thermophilus HB8]]
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==Reference==
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[[Category: Arnold E]]
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The RNA polymerase "switch region" is a target for inhibitors., Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH, Cell. 2008 Oct 17;135(2):295-307. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18957204 18957204]
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[[Category: Das K]]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Protein complex]]
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[[Category: Thermus thermophilus hb8]]
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[[Category: Arnold, E.]]
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[[Category: Das, K.]]
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[[Category: Corallopyronin]]
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[[Category: Crystallography]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed rna polymerase]]
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[[Category: Drug complex]]
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[[Category: Hemihedral]]
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[[Category: Holoenzyme]]
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[[Category: Inhibitor]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Ripostatin]]
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[[Category: Rna polymerase]]
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[[Category: Rnap]]
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[[Category: Sigma factor]]
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[[Category: Transcription]]
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[[Category: Transcription regulation]]
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[[Category: Transferase]]
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[[Category: Twinning]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 12 20:11:38 2008''
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Current revision

Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin

PDB ID 3dxj

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