|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==HMGD(M13A)-DNA complex== | | ==HMGD(M13A)-DNA complex== |
| - | <StructureSection load='3nm9' size='340' side='right' caption='[[3nm9]], [[Resolution|resolution]] 2.85Å' scene=''> | + | <StructureSection load='3nm9' size='340' side='right'caption='[[3nm9]], [[Resolution|resolution]] 2.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nm9]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NM9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nm9]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NM9 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qrv|1qrv]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CG17950, HmgD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=3nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nm9 OCA], [https://pdbe.org/3nm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nm9 RCSB], [https://www.ebi.ac.uk/pdbsum/3nm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nm9 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nm9 OCA], [http://pdbe.org/3nm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nm9 RCSB], [http://www.ebi.ac.uk/pdbsum/3nm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nm9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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/nm/3nm9_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/3nm9_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> |
| Line 36: |
Line 35: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Drome]] | + | [[Category: Drosophila melanogaster]] |
| - | [[Category: Churchill, M E.A]] | + | [[Category: Large Structures]] |
| - | [[Category: Klass, J]] | + | [[Category: Churchill MEA]] |
| - | [[Category: Zoetewey, D L]] | + | [[Category: Klass J]] |
| - | [[Category: Chromosomal protein]] | + | [[Category: Zoetewey DL]] |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Dna bending]]
| + | |
| - | [[Category: Gene regulation-dna complex]]
| + | |
| - | [[Category: High mobility group]]
| + | |
| - | [[Category: Hmg domain]]
| + | |
| - | [[Category: Non-sequence-specific]]
| + | |
| Structural highlights
Function
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.[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 PubMed
The ubiquitous, eukaryotic, high-mobility group box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor-groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity, and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 A. The six proteins and 50 bp of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1 box A-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending.
Structural Analysis of HMGD-DNA Complexes Reveals Influence of Intercalation on Sequence Selectivity and DNA Bending.,Churchill ME, Klass J, Zoetewey DL J Mol Biol. 2010 Aug 25. PMID:20800069[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wagner CR, Hamana K, Elgin SC. A high-mobility-group protein and its cDNAs from Drosophila melanogaster. Mol Cell Biol. 1992 May;12(5):1915-23. PMID:1373803
- ↑ Ner SS, Travers AA. HMG-D, the Drosophila melanogaster homologue of HMG 1 protein, is associated with early embryonic chromatin in the absence of histone H1. EMBO J. 1994 Apr 15;13(8):1817-22. PMID:8168480
- ↑ Churchill ME, Jones DN, Glaser T, Hefner H, Searles MA, Travers AA. HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG. EMBO J. 1995 Mar 15;14(6):1264-75. PMID:7720717
- ↑ Churchill ME, Klass J, Zoetewey DL. Structural Analysis of HMGD-DNA Complexes Reveals Influence of Intercalation on Sequence Selectivity and DNA Bending. J Mol Biol. 2010 Aug 25. PMID:20800069 doi:10.1016/j.jmb.2010.08.031
|
