1e7j: Difference between revisions
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< | ==HMG-D complexed to a bulge DNA== | ||
<StructureSection load='1e7j' size='340' side='right'caption='[[1e7j]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1e7j]] is a 3 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=1E7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E7J 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=1e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7j OCA], [https://pdbe.org/1e7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e7j RCSB], [https://www.ebi.ac.uk/pdbsum/1e7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e7j ProSAT]</span></td></tr> | ||
</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 == | |||
[[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/e7/1e7j_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=1e7j ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
An NMR model is presented for the structure of HMG-D, one of the DROSOPHILA: counterparts of mammalian HMG1/2 proteins, bound to a particular distorted DNA structure, a dA(2) DNA bulge. The complex is in fast to intermediate exchange on the NMR chemical shift time scale and suffers substantial linebroadening for the majority of interfacial resonances. This essentially precludes determination of a high-resolution structure for the interface based on NMR data alone. However, by introducing a small number of additional constraints based on chemical shift and linewidth footprinting combined with analogies to known structures, an ensemble of model structures was generated using a computational strategy equivalent to that for a conventional NMR structure determination. We find that the base pair adjacent to the dA(2) bulge is not formed and that the protein recognizes this feature in forming the complex; intermolecular NOE enhancements are observed from the sidechain of Thr 33 to all four nucleotides of the DNA sequence step adjacent to the bulge. Our results form the first experimental demonstration that when binding to deformed DNA, non-sequence-specific HMG proteins recognize the junction between duplex and nonduplex DNA. Similarities and differences of the present structural model relative to other HMG-DNA complex structures are discussed. | |||
HMG-D complexed to a bulge DNA: an NMR model.,Cerdan R, Payet D, Yang JC, Travers AA, Neuhaus D Protein Sci. 2001 Mar;10(3):504-18. PMID:11344319<ref>PMID:11344319</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1e7j" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[High mobility group protein|High mobility group protein]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Drosophila melanogaster]] | [[Category: Drosophila melanogaster]] | ||
[[Category: Cerdan | [[Category: Large Structures]] | ||
[[Category: Neuhaus | [[Category: Cerdan R]] | ||
[[Category: Payet | [[Category: Neuhaus D]] | ||
[[Category: Travers | [[Category: Payet D]] | ||
[[Category: Yang | [[Category: Travers AA]] | ||
[[Category: Yang J-C]] | |||
Latest revision as of 08:29, 15 May 2024
HMG-D complexed to a bulge DNAHMG-D complexed to a bulge DNA
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 PubMedAn NMR model is presented for the structure of HMG-D, one of the DROSOPHILA: counterparts of mammalian HMG1/2 proteins, bound to a particular distorted DNA structure, a dA(2) DNA bulge. The complex is in fast to intermediate exchange on the NMR chemical shift time scale and suffers substantial linebroadening for the majority of interfacial resonances. This essentially precludes determination of a high-resolution structure for the interface based on NMR data alone. However, by introducing a small number of additional constraints based on chemical shift and linewidth footprinting combined with analogies to known structures, an ensemble of model structures was generated using a computational strategy equivalent to that for a conventional NMR structure determination. We find that the base pair adjacent to the dA(2) bulge is not formed and that the protein recognizes this feature in forming the complex; intermolecular NOE enhancements are observed from the sidechain of Thr 33 to all four nucleotides of the DNA sequence step adjacent to the bulge. Our results form the first experimental demonstration that when binding to deformed DNA, non-sequence-specific HMG proteins recognize the junction between duplex and nonduplex DNA. Similarities and differences of the present structural model relative to other HMG-DNA complex structures are discussed. HMG-D complexed to a bulge DNA: an NMR model.,Cerdan R, Payet D, Yang JC, Travers AA, Neuhaus D Protein Sci. 2001 Mar;10(3):504-18. PMID:11344319[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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