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==Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA== | |||
<StructureSection load='1j5n' size='340' side='right'caption='[[1j5n]]' scene=''> | |||
== Structural highlights == | |||
| | <table><tr><td colspan='2'>[[1j5n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J5N 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=1j5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5n OCA], [https://pdbe.org/1j5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j5n RCSB], [https://www.ebi.ac.uk/pdbsum/1j5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j5n ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
''' | [https://www.uniprot.org/uniprot/NHP6A_YEAST NHP6A_YEAST] DNA-binding protein that induces severe bending of DNA. Required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. Also augments the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. Required for transcriptional initiation fidelity of some but not all tRNA genes. Seems to be functionally redundant with NHP6B.<ref>PMID:7721780</ref> <ref>PMID:8946917</ref> <ref>PMID:11118215</ref> <ref>PMID:11432837</ref> <ref>PMID:11239460</ref> <ref>PMID:11287614</ref> <ref>PMID:12952948</ref> <ref>PMID:14585989</ref> <ref>PMID:15082784</ref> <ref>PMID:15987999</ref> <ref>PMID:16407207</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/j5/1j5n_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=1j5n ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces cerevisiae which belongs to the HMGB protein family. Previously, we have solved the structure of NHP6A in the absence of DNA and modeled its interaction with DNA. Here, we present the refined solution structures of the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and bound forms of the protein adopt the typical L-shaped HMGB domain fold. The DNA in the complex undergoes significant structural rearrangement from its free form while the protein shows smaller but significant conformational changes in the complex. Structural and mutational analysis as well as comparison of the complex with the free DNA provides insight into the factors that contribute to binding site selection and DNA deformations in the complex. Further insight into the amino acid determinants of DNA binding by HMGB domain proteins is given by a correlation study of NHP6A and 32 other HMGB domains belonging to both the DNA-sequence-specific and non-sequence-specific families of HMGB proteins. The resulting correlations can be rationalized by comparison of solved structures of HMGB proteins. | NHP6A is a non-sequence-specific DNA-binding protein from Saccharomyces cerevisiae which belongs to the HMGB protein family. Previously, we have solved the structure of NHP6A in the absence of DNA and modeled its interaction with DNA. Here, we present the refined solution structures of the NHP6A-DNA complex as well as the free 15bp DNA. Both the free and bound forms of the protein adopt the typical L-shaped HMGB domain fold. The DNA in the complex undergoes significant structural rearrangement from its free form while the protein shows smaller but significant conformational changes in the complex. Structural and mutational analysis as well as comparison of the complex with the free DNA provides insight into the factors that contribute to binding site selection and DNA deformations in the complex. Further insight into the amino acid determinants of DNA binding by HMGB domain proteins is given by a correlation study of NHP6A and 32 other HMGB domains belonging to both the DNA-sequence-specific and non-sequence-specific families of HMGB proteins. The resulting correlations can be rationalized by comparison of solved structures of HMGB proteins. | ||
The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding.,Masse JE, Wong B, Yen YM, Allain FH, Johnson RC, Feigon J J Mol Biol. 2002 Oct 18;323(2):263-84. PMID:12381320<ref>PMID:12381320</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1j5n" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Allain FH-T]] | |||
[[Category: Allain | [[Category: Feigon J]] | ||
[[Category: Feigon | [[Category: Johnson RC]] | ||
[[Category: Johnson | [[Category: Masse JE]] | ||
[[Category: Masse | [[Category: Wong B]] | ||
[[Category: Wong | [[Category: Yen Y-M]] | ||
[[Category: Yen | |||