2a6h

From Proteopedia

(Difference between revisions)

Revision as of 23:42, 24 December 2014

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin

Structural highlights

2a6h is a 12 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1iw7, 1smy, 2a68, 2a69, 2a6e
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, RCSB, PDBsum, TOPSAN

Function

[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). [RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOC_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOB_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [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]

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

Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is located 20 A away from the RNAP active site and encompasses the bridge helix and the trigger loop, two elements that are considered to be crucial for RNAP catalytic center function. Structure-based biochemical experiments revealed additional determinants of Stl binding and demonstrated that Stl does not affect NTP substrate binding, DNA translocation, and phosphodiester bond formation. The RNAP-Stl complex structure, its comparison with the closely related substrate bound eukaryotic transcription elongation complexes, and biochemical analysis suggest an inhibitory mechanism in which Stl stabilizes catalytically inactive (preinsertion) substrate bound transcription intermediate, thereby blocking structural isomerization of RNAP to an active configuration. The results provide a basis for a design of new antibiotics utilizing the Stl-like mechanism.

Structural basis of transcription inhibition by antibiotic streptolydigin.,Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG Mol Cell. 2005 Sep 2;19(5):655-66. PMID:16167380^[1]

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

References

↑ Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell. 2005 Sep 2;19(5):655-66. PMID:16167380

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2a6h"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2a6h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6H FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=STD:STREPTOLYDIGIN'>STD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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=STD:STREPTOLYDIGIN'>STD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1iw7|1iw7]], [[1smy|1smy]], [[2a68|2a68]], [[2a69|2a69]], [[2a6e|2a6e]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1iw7|1iw7]], [[1smy|1smy]], [[2a68|2a68]], [[2a69|2a69]], [[2a6e|2a6e]]</td></tr>
-<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a6h RCSB], [http://www.ebi.ac.uk/pdbsum/2a6h PDBsum], [http://www.topsan.org/Proteins/RSGI/2a6h TOPSAN]</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=2a6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a6h RCSB], [http://www.ebi.ac.uk/pdbsum/2a6h PDBsum], [http://www.topsan.org/Proteins/RSGI/2a6h TOPSAN]</span></td></tr>
-<table>
+</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]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 37: @@
 [[Category: DNA-directed RNA polymerase]]
 [[Category: Thermus thermophilus]]
-[[Category: Igarashi, N.]]
+[[Category: Igarashi, N]]
-[[Category: Matsugaki, N.]]
+[[Category: Matsugaki, N]]
-[[Category: Nikiforov, V.]]
+[[Category: Nikiforov, V]]
-[[Category: Perederina, A.]]
+[[Category: Perederina, A]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Structural genomic]]
-[[Category: Savkina, M.]]
+[[Category: Savkina, M]]
-[[Category: Severinov, K.]]
+[[Category: Severinov, K]]
-[[Category: Tahirov, T H.]]
+[[Category: Tahirov, T H]]
-[[Category: Temiakov, D.]]
+[[Category: Temiakov, D]]
-[[Category: Vassylyev, D G.]]
+[[Category: Vassylyev, D G]]
-[[Category: Vassylyeva, M N.]]
+[[Category: Vassylyeva, M N]]
-[[Category: Wakatsuki, S.]]
+[[Category: Wakatsuki, S]]
-[[Category: Zenkin, N.]]
+[[Category: Zenkin, N]]
-[[Category: Zorov, S.]]
+[[Category: Zorov, S]]
 [[Category: Antibiotic]]
-[[Category: Riken structural genomics/proteomics initiative]]
 [[Category: Rna polymerase holoenzyme]]
 [[Category: Rsgi]]
 [[Category: Streptolydigin]]
-[[Category: Structural genomic]]
 [[Category: Transcription regulation]]
 [[Category: Transferase]]

2a6h

From Proteopedia

Revision as of 23:42, 24 December 2014

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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