3u6y

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==Crystal structure of ALBA2-DNA complex==
==Crystal structure of ALBA2-DNA complex==
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<StructureSection load='3u6y' size='340' side='right' caption='[[3u6y]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='3u6y' size='340' side='right'caption='[[3u6y]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3u6y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U6Y FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3u6y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U6Y FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</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&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2h9u|2h9u]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">albA2, APE_1823 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 Aeropyrum pernix])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3u6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u6y OCA], [https://pdbe.org/3u6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u6y RCSB], [https://www.ebi.ac.uk/pdbsum/3u6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u6y ProSAT]</span></td></tr>
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<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=3u6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u6y RCSB], [http://www.ebi.ac.uk/pdbsum/3u6y PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE]] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).
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[https://www.uniprot.org/uniprot/ALBA2_AERPE ALBA2_AERPE] Binds double-stranded DNA tightly but without sequence specificity. It is distributed uniformly and abundantly on the chromosome, suggesting a role in chromatin architecture. However, it does not significantly compact DNA. Binds rRNA and mRNA in vivo. May play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes (By similarity).
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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DNA binding proteins are essential in all organisms, and they play important roles in both compacting and regulating the genetic material. All thermophilic and hyperthermophilic archaea encode one or more copies of Alba or Sso10b, which is a small, abundant, basic protein that binds DNA. Here, we present the crystal structure of Ape10b2 from Aeropyrum pernix K1 at 1.70 A. Although the overall structure resembles the known Alba protein fold, a significant conformational change was observed in the loop regions. Specifically, the L5 loop is slightly longer, as compared to those of other known proteins, and the flexibility of this loop may facilitate the interaction with double stranded DNA. In addition, we showed that Ape10b2 binds to 16 and 39 bp duplex DNAs with high affinity. On the basis of our analyses, we have created a putative protein-DNA complex model.
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All thermophilic and hyperthermophilic archaea encode homologs of dimeric Alba (Sac10b) proteins that bind cooperatively at high density to DNA. Here, we report the 2.0 A resolution crystal structure of an Alba2 (Ape10b2)-dsDNA complex from Aeropyrum pernix K1. A rectangular tube-like structure encompassing duplex DNA reveals the positively charged residues in the monomer-monomer interface of each dimer packing on either side of the bound dsDNA in successive minor grooves. The extended hairpin loop connecting strands beta3 and beta4 undergoes significant conformational changes upon DNA binding to accommodate the other Alba2 dimer during oligomerization. Mutational analysis of key interacting residues confirmed the specificity of Alba2-dsDNA interactions.
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Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.,Kumarevel T, Sakamoto K, Gopinath SC, Shinkai A, Kumar PK, Yokoyama S Proteins. 2008 May 15;71(3):1156-62. PMID:18004791<ref>PMID:18004791</ref>
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Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1.,Tanaka T, Padavattan S, Kumarevel T J Biol Chem. 2012 Mar 23;287(13):10394-402. Epub 2012 Feb 10. PMID:22334696<ref>PMID:22334696</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3u6y" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aeropyrum pernix]]
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[[Category: Aeropyrum pernix K1]]
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[[Category: Kumarevel, T]]
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[[Category: Large Structures]]
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[[Category: Structural genomic]]
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[[Category: Synthetic construct]]
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[[Category: Tanaka, T]]
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[[Category: Kumarevel T]]
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[[Category: Alba 2]]
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[[Category: Tanaka T]]
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[[Category: Archaea]]
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[[Category: Dna binding protein-dna complex]]
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[[Category: Dna-binding protein]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Rsgi]]
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Current revision

Crystal structure of ALBA2-DNA complex

PDB ID 3u6y

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