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| | ==Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A== | | ==Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A== |
| - | <StructureSection load='1lwm' size='340' side='right' caption='[[1lwm]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='1lwm' size='340' side='right'caption='[[1lwm]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1lwm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1lwm]] is a 1 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=1LWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWM FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1cg7|1cg7]], [[1j5n|1j5n]], [[1lwa|1lwa]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NHP6A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1lwm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwm OCA], [https://pdbe.org/1lwm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwm RCSB], [https://www.ebi.ac.uk/pdbsum/1lwm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwm 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=1lwm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwm OCA], [http://pdbe.org/1lwm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwm RCSB], [http://www.ebi.ac.uk/pdbsum/1lwm PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == 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/lw/1lwm_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwm_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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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=1lwm 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | + | [[Category: Large Structures]] |
| - | [[Category: Allain, F H.T]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Feigon, J]] | + | [[Category: Allain FH-T]] |
| - | [[Category: Johnson, R C]] | + | [[Category: Feigon J]] |
| - | [[Category: Masse, J E]] | + | [[Category: Johnson RC]] |
| - | [[Category: Wong, B]] | + | [[Category: Masse JE]] |
| - | [[Category: Yen, Y M]] | + | [[Category: Wong B]] |
| - | [[Category: Alpha helix]]
| + | [[Category: Yen Y-M]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Hmg-box]]
| + | |
| - | [[Category: Hmgb]]
| + | |
| Structural highlights
Function
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.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]
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
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[12]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Paull TT, Johnson RC. DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. Consequences for nucleoprotein complex assembly and chromatin condensation. J Biol Chem. 1995 Apr 14;270(15):8744-54. PMID:7721780
- ↑ Paull TT, Carey M, Johnson RC. Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. Genes Dev. 1996 Nov 1;10(21):2769-81. PMID:8946917
- ↑ Moreira JM, Holmberg S. Chromatin-mediated transcriptional regulation by the yeast architectural factors NHP6A and NHP6B. EMBO J. 2000 Dec 15;19(24):6804-13. PMID:11118215 doi:http://dx.doi.org/10.1093/emboj/19.24.6804
- ↑ Formosa T, Eriksson P, Wittmeyer J, Ginn J, Yu Y, Stillman DJ. Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. EMBO J. 2001 Jul 2;20(13):3506-17. PMID:11432837 doi:http://dx.doi.org/10.1093/emboj/20.13.3506
- ↑ Kruppa M, Moir RD, Kolodrubetz D, Willis IM. Nhp6, an HMG1 protein, functions in SNR6 transcription by RNA polymerase III in S. cerevisiae. Mol Cell. 2001 Feb;7(2):309-18. PMID:11239460
- ↑ Lopez S, Livingstone-Zatchej M, Jourdain S, Thoma F, Sentenac A, Marsolier MC. High-mobility-group proteins NHP6A and NHP6B participate in activation of the RNA polymerase III SNR6 gene. Mol Cell Biol. 2001 May;21(9):3096-104. PMID:11287614 doi:http://dx.doi.org/10.1128/MCB.21.9.3096-3104.2001
- ↑ Ruone S, Rhoades AR, Formosa T. Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. J Biol Chem. 2003 Nov 14;278(46):45288-95. Epub 2003 Sep 1. PMID:12952948 doi:http://dx.doi.org/10.1074/jbc.M307291200
- ↑ Mason PB, Struhl K. The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol. 2003 Nov;23(22):8323-33. PMID:14585989
- ↑ Rhoades AR, Ruone S, Formosa T. Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6. Mol Cell Biol. 2004 May;24(9):3907-17. PMID:15082784
- ↑ Biswas D, Yu Y, Prall M, Formosa T, Stillman DJ. The yeast FACT complex has a role in transcriptional initiation. Mol Cell Biol. 2005 Jul;25(14):5812-22. PMID:15987999 doi:http://dx.doi.org/25/14/5812
- ↑ Kassavetis GA, Steiner DF. Nhp6 is a transcriptional initiation fidelity factor for RNA polymerase III transcription in vitro and in vivo. J Biol Chem. 2006 Mar 17;281(11):7445-51. Epub 2006 Jan 11. PMID:16407207 doi:http://dx.doi.org/10.1074/jbc.M512810200
- ↑ Masse JE, Wong B, Yen YM, Allain FH, Johnson RC, Feigon J. The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding. J Mol Biol. 2002 Oct 18;323(2):263-84. PMID:12381320
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