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1e7j

From Proteopedia

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HMG-D complexed to a bulge DNA

Structural highlights

1e7j is a 3 chain structure with sequence from Drosophila melanogaster. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ Cerdan R, Payet D, Yang JC, Travers AA, Neuhaus D. HMG-D complexed to a bulge DNA: an NMR model. Protein Sci. 2001 Mar;10(3):504-18. PMID:11344319

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1e7j"

@@ Line 1: / Line 1: @@
-==HMG-D COMPLEXED TO A BULGE DNA==
-<StructureSection load='1e7j' size='340' side='right' caption='[[1e7j]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+==HMG-D complexed to a bulge DNA==
+<StructureSection load='1e7j' size='340' side='right'caption='[[1e7j]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1e7j]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E7J FirstGlance]. <br>
+<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='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">Solution NMR</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=1e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7j OCA], [http://pdbe.org/1e7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e7j RCSB], [http://www.ebi.ac.uk/pdbsum/1e7j PDBsum]</span></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 ==
-[[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 ==
 [[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>
+    <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>
@@ Line 34: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Drosophila melanogaster]]
-[[Category: Cerdan, R]]
+[[Category: Large Structures]]
-[[Category: Neuhaus, D]]
+[[Category: Cerdan R]]
-[[Category: Payet, D]]
+[[Category: Neuhaus D]]
-[[Category: Travers, A A]]
+[[Category: Payet D]]
-[[Category: Yang, J C]]
+[[Category: Travers AA]]
-[[Category: Protein-dna complex]]
+[[Category: Yang J-C]]
-[[Category: Protein/dna]]

1e7j

From Proteopedia

Current revision

HMG-D complexed to a bulge DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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