2be5: Difference between revisions

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Revision as of 17:00, 20 March 2008

File:2be5.gif

, resolution 2.40Å

Ligands:

, and

Activity:

DNA-directed RNA polymerase, with EC number 2.7.7.6

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin

OverviewOverview

Tagetitoxin (Tgt) inhibits transcription by an unknown mechanism. A structure at a resolution of 2.4 A of the Thermus thermophilus RNA polymerase (RNAP)-Tgt complex revealed that the Tgt-binding site within the RNAP secondary channel overlaps that of the stringent control effector ppGpp, which partially protects RNAP from Tgt inhibition. Tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to Tgt in vitro. Importantly, a Tgt phosphate, together with two active site acidic residues, coordinates the third Mg(2+) ion, which is distinct from the two catalytic metal ions. We show that Tgt inhibits all RNAP catalytic reactions and propose a mechanism in which the Tgt-bound Mg(2+) ion has a key role in stabilization of an inactive transcription intermediate. Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes.

About this StructureAbout this Structure

2BE5 is a Protein complex structure of sequences from Thermus thermophilus. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for transcription inhibition by tagetitoxin., Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I, Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. Epub 2005 Nov 6. PMID:16273103

Page seeded by OCA on Thu Mar 20 16:00:45 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2be5.gif|left|200px]]<br /><applet load="2be5" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2be5.gif|left|200px]]
-caption="2be5, resolution 2.40&Aring;" />
-'''Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin'''<br />
+ {{Structure
+|PDB= 2be5 |SIZE=350|CAPTION= <scene name='initialview01'>2be5</scene>, resolution 2.40&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=TGT:TAGETITOXIN'>TGT</scene>
+|ACTIVITY= [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]
+|GENE=
+}}
+'''Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-BE5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=TGT:'>TGT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BE5 OCA].
+BE5 is a [[Protein complex]] structure of sequences 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=2BE5 OCA].
 ==Reference==
-Structural basis for transcription inhibition by tagetitoxin., Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I, Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. Epub 2005 Nov 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16273103 16273103]
+Structural basis for transcription inhibition by tagetitoxin., Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I, Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. Epub 2005 Nov 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16273103 16273103]
 [[Category: DNA-directed RNA polymerase]]
 [[Category: Protein complex]]
@@ Line 30: / Line 39: @@
 [[Category: rna polymerase holoenzyme]]
 [[Category: rsgi]]
-[[Category: structural genomics]]
+[[Category: structural genomic]]
 [[Category: tagetitoxin]]
 [[Category: transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:36:50 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:00:45 2008''