3dxj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3dxj" [edit=sysop:move=sysop])
Current revision (12:54, 30 August 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3dxj.png|left|200px]]
 
-
{{STRUCTURE_3dxj| PDB=3dxj | SCENE= }}
+
==Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin==
 +
<StructureSection load='3dxj' size='340' side='right'caption='[[3dxj]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
<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>
 +
</table>
 +
== Function ==
 +
[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.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dx/3dxj_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
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.
-
===Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin===
+
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>
-
{{ABSTRACT_PUBMED_18957204}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 3dxj" style="background-color:#fffaf0;"></div>
-
[[3dxj]] is a 12 chain structure of [[RNA polymerase]] with sequence 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].
+
==See Also==
==See Also==
-
*[[RNA polymerase|RNA polymerase]]
+
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-
 
+
*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-
==Reference==
+
== References ==
-
<ref group="xtra">PMID:018957204</ref><references group="xtra"/>
+
<references/>
-
[[Category: DNA-directed RNA polymerase]]
+
__TOC__
-
[[Category: Thermus thermophilus hb8]]
+
</StructureSection>
-
[[Category: Arnold, E.]]
+
[[Category: Large Structures]]
-
[[Category: Das, K.]]
+
[[Category: Thermus thermophilus HB8]]
-
[[Category: Corallopyronin]]
+
[[Category: Arnold E]]
-
[[Category: Crystallography]]
+
[[Category: Das K]]
-
[[Category: Dna-binding]]
+
-
[[Category: Dna-directed rna polymerase]]
+
-
[[Category: Drug complex]]
+
-
[[Category: Hemihedral]]
+
-
[[Category: Holoenzyme]]
+
-
[[Category: Inhibitor]]
+
-
[[Category: Nucleotidyltransferase]]
+
-
[[Category: Ripostatin]]
+
-
[[Category: Rna polymerase]]
+
-
[[Category: Rnap]]
+
-
[[Category: Sigma factor]]
+
-
[[Category: Transcription]]
+
-
[[Category: Transcription regulation]]
+
-
[[Category: Transferase]]
+
-
[[Category: Twinning]]
+

Current revision

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

PDB ID 3dxj

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3dxj"
Personal tools