1hma: Difference between revisions
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==THE SOLUTION STRUCTURE AND DYNAMICS OF THE DNA BINDING DOMAIN OF HMG-D FROM DROSOPHILA MELANOGASTER== | ==THE SOLUTION STRUCTURE AND DYNAMICS OF THE DNA BINDING DOMAIN OF HMG-D FROM DROSOPHILA MELANOGASTER== | ||
<StructureSection load='1hma' size='340' side='right' caption='[[1hma | <StructureSection load='1hma' size='340' side='right'caption='[[1hma]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1hma]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1hma]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HMA FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </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=1hma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hma OCA], [https://pdbe.org/1hma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hma RCSB], [https://www.ebi.ac.uk/pdbsum/1hma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hma ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/HMGD_DROME HMGD_DROME] Binds preferentially single-stranded DNA and unwinds double stranded DNA. Prefers sites containing the sequence 5'-ttg-3'. Facilitates DNA bending. Associated with early embryonic chromatin in the absence of histone H1.<ref>PMID:1373803</ref> <ref>PMID:8168480</ref> <ref>PMID:7720717</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/1hma_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/1hma_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=1hma ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1hma" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[High mobility group protein|High mobility group protein]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Drosophila melanogaster]] | [[Category: Drosophila melanogaster]] | ||
[[Category: Churchill | [[Category: Large Structures]] | ||
[[Category: Jones | [[Category: Churchill MEA]] | ||
[[Category: Keeler | [[Category: Jones DNM]] | ||
[[Category: Ner | [[Category: Keeler J]] | ||
[[Category: Neuhaus | [[Category: Ner SS]] | ||
[[Category: Searles | [[Category: Neuhaus D]] | ||
[[Category: Shaw | [[Category: Searles MA]] | ||
[[Category: Travers | [[Category: Shaw GL]] | ||
[[Category: Travers AA]] | |||
Latest revision as of 11:32, 22 May 2024
THE SOLUTION STRUCTURE AND DYNAMICS OF THE DNA BINDING DOMAIN OF HMG-D FROM DROSOPHILA MELANOGASTERTHE SOLUTION STRUCTURE AND DYNAMICS OF THE DNA BINDING DOMAIN OF HMG-D FROM DROSOPHILA MELANOGASTER
Structural highlights
FunctionHMGD_DROME Binds preferentially single-stranded DNA and unwinds double stranded DNA. Prefers sites containing the sequence 5'-ttg-3'. Facilitates DNA bending. Associated with early embryonic chromatin in the absence of histone H1.[1] [2] [3] 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 PubMedBACKGROUND: The HMG-box is a conserved DNA-binding motif that has been identified in many high mobility group (HMG) proteins. HMG-D is a non-histone chromosomal protein from Drosophila melanogaster that is closely related to the mammalian HMG-box proteins HMG-1 and HMG-2. Previous structures determined for an HMG-box domain from rat and hamster exhibit the same global topology, but differ significantly in detail. It has been suggested that these differences may arise from hinge motions which allow the protein to adapt to the shape of its target DNA. RESULTS: We present the solution structure of HMG-D determined by NMR spectroscopy to an overall precision of 0.85 A root mean squared deviation (rmsd) for the backbone atoms. The protein consists of an extended amino-terminal region and three alpha-helices that fold into a characteristic 'L' shape. The central core region of the molecule is highly stable and maintains an angle of approximately 80 degrees between the axes of helices 2 and 3. The backbone dynamics determined from 15N NMR relaxation measurements show a high correlation with the mean residue rmsd determined from the calculated structures. CONCLUSIONS: The structure determined for the HMG-box motif from HMG-D is essentially identical to the structure determined for the B-domain of mammalian HMG-1. Since these proteins have significantly different sequences our results indicate that the global fold and the mode of interaction with DNA are also likely to be conserved in all eukaryotes. The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster.,Jones DN, Searles MA, Shaw GL, Churchill ME, Ner SS, Keeler J, Travers AA, Neuhaus D Structure. 1994 Jul 15;2(7):609-27. PMID:7922039[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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