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1wtu
From Proteopedia
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| - | [[Image:1wtu.jpg|left|200px]] | ||
| - | + | ==TRANSCRIPTION FACTOR 1, NMR, MINIMIZED AVERAGE STRUCTURE== | |
| - | + | <StructureSection load='1wtu' size='340' side='right'caption='[[1wtu]]' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[1wtu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_SPO1 Bacillus virus SPO1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WTU FirstGlance]. <br> | |
| - | | | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1wtu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wtu OCA], [https://pdbe.org/1wtu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wtu RCSB], [https://www.ebi.ac.uk/pdbsum/1wtu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wtu ProSAT]</span></td></tr> | |
| - | + | </table> | |
| - | + | == Function == | |
| - | + | [https://www.uniprot.org/uniprot/TF1_BPSP1 TF1_BPSP1] Selectively binds to and inhibits the transcription of hydroxymethyluracil-(hmUra)-containing DNA, such as SP01 DNA, by RNA polymerase in vitro. | |
| - | + | == 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/wt/1wtu_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=1wtu ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
The solution structure of a type II DNA-binding protein, the bacteriophage SPO1-encoded transcription factor 1 (TF1), was determined using NMR spectroscopy. Selective 2H-labeling, 13C-labeling and isotopic heterodimers were used to distinguish contacts between and within monomers of the dimeric protein. A total of 1914 distance and dihedral angle constraints derived from NMR experiments were used in structure calculations using restrained molecular dynamics and simulated annealing protocols. The ensemble of 30 calculated structures has a root-mean-square deviation (r.m.s.d.) of 0.9 A, about the average structure for the backbone atoms, and 1.2 A for all heavy-atoms of the dimeric core (helices 1 and 2) and the beta-sheets. A severe helix distortion at residues 92-93 in the middle of helix 3 is associated with r.m.s.d. of approximately 1.5 A for the helix 3 backbone. Deviations of approximately 5 A or larger are noted for the very flexible beta-ribbon arms that constitute part of a proposed DNA-binding region. A structural model of TF1 has been calculated based on the previously reported crystal structure of the homologous HU protein and this model was used as the starting structure for calculations. A comparison between the calculated average solution structure of TF1 and a solution structure of HU indicates a similarity in the dimeric core (excluding the nine amino acid residue tail) with pairwise deviations of 2 to 3 A. The largest deviations between the average structure and the HU solution structure were found in the beta-ribbon arms, as expected. A 4 A deviation is found at residue 15 of TF1 which is in a loop connecting two helical segments; it has been reported that substitution of Glu15 by Gly increases the thermostability of TF1. The homology between TF1 and other proteins of this family leads us to anticipate similar tertiary structures. | The solution structure of a type II DNA-binding protein, the bacteriophage SPO1-encoded transcription factor 1 (TF1), was determined using NMR spectroscopy. Selective 2H-labeling, 13C-labeling and isotopic heterodimers were used to distinguish contacts between and within monomers of the dimeric protein. A total of 1914 distance and dihedral angle constraints derived from NMR experiments were used in structure calculations using restrained molecular dynamics and simulated annealing protocols. The ensemble of 30 calculated structures has a root-mean-square deviation (r.m.s.d.) of 0.9 A, about the average structure for the backbone atoms, and 1.2 A for all heavy-atoms of the dimeric core (helices 1 and 2) and the beta-sheets. A severe helix distortion at residues 92-93 in the middle of helix 3 is associated with r.m.s.d. of approximately 1.5 A for the helix 3 backbone. Deviations of approximately 5 A or larger are noted for the very flexible beta-ribbon arms that constitute part of a proposed DNA-binding region. A structural model of TF1 has been calculated based on the previously reported crystal structure of the homologous HU protein and this model was used as the starting structure for calculations. A comparison between the calculated average solution structure of TF1 and a solution structure of HU indicates a similarity in the dimeric core (excluding the nine amino acid residue tail) with pairwise deviations of 2 to 3 A. The largest deviations between the average structure and the HU solution structure were found in the beta-ribbon arms, as expected. A 4 A deviation is found at residue 15 of TF1 which is in a loop connecting two helical segments; it has been reported that substitution of Glu15 by Gly increases the thermostability of TF1. The homology between TF1 and other proteins of this family leads us to anticipate similar tertiary structures. | ||
| - | + | Structure of the Bacillus subtilis phage SPO1-encoded type II DNA-binding protein TF1 in solution.,Jia X, Grove A, Ivancic M, Hsu VL, Geiduscheck EP, Kearns DR J Mol Biol. 1996 Oct 25;263(2):259-68. PMID:8913305<ref>PMID:8913305</ref> | |
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| - | Structure of the Bacillus subtilis phage SPO1-encoded type II DNA-binding protein TF1 in solution., Jia X, Grove A, Ivancic M, Hsu VL, Geiduscheck EP, Kearns DR | + | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 1wtu" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bacillus virus SPO1]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Geiduschek EP]] | ||
| + | [[Category: Grove A]] | ||
| + | [[Category: Hsu VL]] | ||
| + | [[Category: Ivancic M]] | ||
| + | [[Category: Jia X]] | ||
| + | [[Category: Kearns DR]] | ||
Current revision
TRANSCRIPTION FACTOR 1, NMR, MINIMIZED AVERAGE STRUCTURE
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