1smy

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[[Image:1smy.gif|left|200px]]<br /><applet load="1smy" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1smy.gif|left|200px]]
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caption="1smy, resolution 2.70&Aring;" />
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'''Structural basis for transcription regulation by alarmone ppGpp'''<br />
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{{Structure
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|PDB= 1smy |SIZE=350|CAPTION= <scene name='initialview01'>1smy</scene>, resolution 2.70&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=G4P:GUANOSINE-5',3'-TETRAPHOSPHATE'>G4P</scene>
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|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]
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|GENE=
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}}
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'''Structural basis for transcription regulation by alarmone ppGpp'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1SMY 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=G4P:'>G4P</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=1SMY OCA].
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1SMY 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=1SMY OCA].
==Reference==
==Reference==
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Structural basis for transcription regulation by alarmone ppGpp., Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG, Cell. 2004 Apr 30;117(3):299-310. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15109491 15109491]
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Structural basis for transcription regulation by alarmone ppGpp., Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG, Cell. 2004 Apr 30;117(3):299-310. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15109491 15109491]
[[Category: DNA-directed RNA polymerase]]
[[Category: DNA-directed RNA polymerase]]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: rna polymerase holoenzyme]]
[[Category: rna polymerase holoenzyme]]
[[Category: rsgi]]
[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: structural genomic]]
[[Category: transcription regulation]]
[[Category: transcription regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:03:09 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:07:05 2008''

Revision as of 12:07, 20 March 2008

Image:1smy.gif


PDB ID 1smy

Drag the structure with the mouse to rotate
, resolution 2.70Å
Ligands: , and
Activity: DNA-directed RNA polymerase, with EC number 2.7.7.6
Coordinates: save as pdb, mmCIF, xml



Structural basis for transcription regulation by alarmone ppGpp


Overview

Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.

About this Structure

1SMY is a Protein complex structure of sequences from Thermus thermophilus. Full crystallographic information is available from OCA.

Reference

Structural basis for transcription regulation by alarmone ppGpp., Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG, Cell. 2004 Apr 30;117(3):299-310. PMID:15109491

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