2h9u

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:50, 25 October 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2h9u.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of the archaea specific DNA binding protein==
-
The line below this paragraph, containing "STRUCTURE_2h9u", creates the "Structure Box" on the page.
+
<StructureSection load='2h9u' size='340' side='right'caption='[[2h9u]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2h9u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9U FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-
{{STRUCTURE_2h9u| PDB=2h9u | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9u OCA], [https://pdbe.org/2h9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9u RCSB], [https://www.ebi.ac.uk/pdbsum/2h9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9u ProSAT], [https://www.topsan.org/Proteins/RSGI/2h9u TOPSAN]</span></td></tr>
-
 
+
</table>
-
'''Crystal structure of the archaea specific DNA binding protein'''
+
== Function ==
-
 
+
[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).
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding affinity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended beta-hairpins flanking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a final binding stoichiometry of approximately 5 bp DNA per Alba dimer. We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h9/2h9u_consurf.spt"</scriptWhenChecked>
-
2H9U is a [[Single protein]] structure of 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=2H9U OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Structure of Alba: an archaeal chromatin protein modulated by acetylation., Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF, EMBO J. 2002 Sep 2;21(17):4654-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198167 12198167]
+
</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=2h9u ConSurf].
-
[[Category: Aeropyrum pernix]]
+
<div style="clear:both"></div>
-
[[Category: Single protein]]
+
__TOC__
-
[[Category: Kumarevel, T S.]]
+
</StructureSection>
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Aeropyrum pernix K1]]
-
[[Category: Sakamoto, K.]]
+
[[Category: Large Structures]]
-
[[Category: Shinkai, A.]]
+
[[Category: Kumarevel TS]]
-
[[Category: Yokoyama, S.]]
+
[[Category: Sakamoto K]]
-
[[Category: Aeropyrum pernix]]
+
[[Category: Shinkai A]]
-
[[Category: Archaea]]
+
[[Category: Yokoyama S]]
-
[[Category: Crystal structure]]
+
-
[[Category: Dna binding protein]]
+
-
[[Category: National project on protein structural and functional analyse]]
+
-
[[Category: Nppsfa]]
+
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Structural genomic]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 06:02:03 2008''
+

Current revision

Crystal structure of the archaea specific DNA binding protein

PDB ID 2h9u

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2h9u"
Personal tools