1dak: Difference between revisions

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-{{Seed}}
-[[Image:1dak.png|left|200px]]
-<!--
+==DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE==
-The line below this paragraph, containing "STRUCTURE_1dak", creates the "Structure Box" on the page.
+<StructureSection load='1dak' size='340' side='right'caption='[[1dak]], [[Resolution|resolution]] 1.60&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'>[[1dak]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DAK 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DPU:MIXED+CARBAMIC+PHOSPHORIC+ACID+ANHYDRIDE+OF+7,8-DIAMINONONANIC+ACID'>DPU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_1dak|  PDB=1dak  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dak OCA], [https://pdbe.org/1dak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dak RCSB], [https://www.ebi.ac.uk/pdbsum/1dak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dak ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BIOD1_ECOLI BIOD1_ECOLI] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.<ref>PMID:4892372</ref> <ref>PMID:4921568</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/da/1dak_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=1dak ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO2 and 7, 8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9- and 1.6-A resolution, respectively, of the enzyme-MgATP-diaminopelargonic acid and enzyme-MgADP-carbamic-phosphoric acid anhydride complexes, observed by using kinetic crystallography. Reaction initiation by addition of either NaHCO3 or diaminopelargonic acid to crystals already containing cosubstrates resulted in the accumulation of the phosphorylated intermediate at the active site. The phosphoryl transfer step shows inversion of the configuration at the phosphorus atom, consistent with an in-line attack by the carbamate oxygen onto the phosphorus atom of ATP. A key feature in the structure of the complex of the enzyme with the reaction intermediate is two magnesium ions, bridging the phosphates at the cleavage site. These magnesium ions compensate the negative charges at both phosphate groups after phosphoryl transfer and contribute to the stabilization of the reaction intermediate.
-===DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE===
+Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.,Kack H, Gibson KJ, Lindqvist Y, Schneider G Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:9576910<ref>PMID:9576910</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1dak" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9576910}}, adds the Publication Abstract to the page
+*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9576910 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9576910}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DAK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAK OCA].
-==Reference==
-Snapshot of a phosphorylated substrate intermediate by kinetic crystallography., Kack H, Gibson KJ, Lindqvist Y, Schneider G, Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9576910 9576910]
-[[Category: Dethiobiotin synthase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Gibson, K J.]]
+[[Category: Gibson KJ]]
-[[Category: Kaeck, H.]]
+[[Category: Kaeck H]]
-[[Category: Lindqvist, Y.]]
+[[Category: Lindqvist Y]]
-[[Category: Schneider, G.]]
+[[Category: Schneider G]]
-[[Category: Atp]]
-[[Category: Biotin biosynthesis]]
-[[Category: Kinetic crystallography]]
-[[Category: Ligase]]
-[[Category: Phoshporyl transfer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:44:54 2008''