3dxj: Difference between revisions

Latest revision as of 12:54, 30 August 2023

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

Structural highlights

3dxj is a 12 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	MG, MPD, NE6, PO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOA_THET8 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. The RNA polymerase "switch region" is a target for inhibitors. Cell. 2008 Oct 17;135(2):295-307. PMID:18957204 doi:10.1016/j.cell.2008.09.033

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OCA

[1] 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. The RNA polymerase "switch region" is a target for inhibitors. Cell. 2008 Oct 17;135(2):295-307. PMID:18957204 doi:10.1016/j.cell.2008.09.033

[1]

@@ Line 3: / Line 3: @@
 <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 [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]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DXJ FirstGlance]. <br>
+<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='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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zyr|1zyr]], [[1iw7|1iw7]]</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='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'>[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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3dxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dxj OCA], [http://pdbe.org/3dxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dxj RCSB], [http://www.ebi.ac.uk/pdbsum/3dxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dxj ProSAT]</span></td></tr>
 </table>
 == 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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: DNA-directed RNA polymerase]]
 [[Category: Large Structures]]
-[[Category: Thermus thermophilus hb8]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Arnold, E]]
+[[Category: Arnold E]]
-[[Category: Das, K]]
+[[Category: Das K]]
-[[Category: Corallopyronin]]
-[[Category: Crystallography]]
-[[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]]

3dxj: Difference between revisions

Latest revision as of 12:54, 30 August 2023

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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