2dxu: Difference between revisions

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-{{Seed}}
-[[Image:2dxu.png|left|200px]]
-<!--
+==Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with Biotinyl-5'-AMP, Mutation R48A==
-The line below this paragraph, containing "STRUCTURE_2dxu", creates the "Structure Box" on the page.
+<StructureSection load='2dxu' size='340' side='right'caption='[[2dxu]], [[Resolution|resolution]] 1.28&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'>[[2dxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXU 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]] 1.28&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BT5:BIOTINYL-5-AMP'>BT5</scene></td></tr>
-{{STRUCTURE_2dxu|  PDB=2dxu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxu OCA], [https://pdbe.org/2dxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxu RCSB], [https://www.ebi.ac.uk/pdbsum/2dxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxu ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxu TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O57883_PYRHO O57883_PYRHO]
+== 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/dx/2dxu_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=2dxu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biotin protein ligase (BPL) catalyzes the biotinylation of the biotin carboxyl carrier protein (BCCP) only at a special lysine residue. Here we report the first structure of BPL.BCCP complex crystals, which are prepared using two BPL mutants: R48A and R48A/K111A. From a detailed structural characterization, it is likely that the mutants retain functionality as enzymes but have a reduced activity to produce the reaction intermediate biotinyl-5'-AMP. The observed biotin and partly disordered ATP in the mutant structures may act as a non-reactive analog of the substrates or biotinyl-5'-AMP, thereby providing the complex crystals. The four crystallographically independent BPL.BCCP complexes obtained can be classified structurally into three groups: the formation stages 1 and 2 with apo-BCCP and the product stage with biotinylated holo-BCCP. Residues responsible for the complex formation as well as for the biotinylation reaction have been identified. The C-terminal domain of BPL shows especially large conformational changes to accommodate BCCP, suggesting its functional importance. The formation stage 1 complex shows the closest distance between the carboxyl carbon of biotin and the special lysine of BCCP, suggesting its relevance to the unobserved reaction stage. Interestingly, bound ATP and biotin are also seen in the product stage, indicating that the substrates may be recruited into the product stage complex before the release of holo-BCCP, probably for the next reaction cycle. The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction.
-===Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with Biotinyl-5'-AMP, Mutation R48A===
+Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate.,Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N J Biol Chem. 2008 May 23;283(21):14739-50. Epub 2008 Mar 26. PMID:18372281<ref>PMID:18372281</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dxu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18372281}}, adds the Publication Abstract to the page
+*[[Biotin Protein Ligase 3D structures|Biotin Protein Ligase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18372281 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18372281}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DXU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXU OCA].
-==Reference==
-Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate., Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N, J Biol Chem. 2008 May 23;283(21):14739-50. Epub 2008 Mar 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18372281 18372281]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
+[[Category: Bagautdinov B]]
-[[Category: Bagautdinov, B.]]
+[[Category: Kunishima N]]
-[[Category: Kunishima, N.]]
+[[Category: Matsuura Y]]
-[[Category: Matsuura, Y.]]
+[[Category: Taketa M]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Taketa, M.]]
-[[Category: Biotin biosynthesis]]
-[[Category: Dimer]]
-[[Category: Ligase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: X-ray diffraction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:01:36 2008''