1dbs: Difference between revisions

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OCA

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-[[Image:1dbs.gif|left|200px]]<br /><applet load="1dbs" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1dbs, resolution 1.8&Aring;" />
-'''MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE'''<br />
-==Overview==
+==MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE==
-BACKGROUND: Biotin is the vitamin essential for many biological, carboxylation reactions, such as the conversion of acetyl-coenzyme A (CoA), to malonyl-CoA in fatty acid biosynthesis. Dethiobiotin synthetase (DTBS), facilitates the penultimate, ureido ring closure in biotin synthesis, which is a non-biotin-dependent carboxylation. DTBS displays no sequence, similarity to any other protein in the database. Structural studies, provide a molecular insight into the reaction mechanism of DTBS. RESULTS:, We present the structure of DTBS refined to 1.80 A resolution with an, R-factor of 17.2% for all terms plus unrefined data on the binding of the, substrate, 7,8-diaminopelargonic acid and the product, dethiobiotin. These, studies confirm that the protein forms a homodimer with each subunit, folded as a single globular alpha/beta domain. The presence of sulphate, ions in the crystals and comparisons with the related Ha-ras-p21 oncogene, product are used to infer the ATP-binding site, corroborated by the, difference electron density for the ATP analogue AMP-PNP. CONCLUSIONS:, This study establishes that the enzyme active site is situated at the, dimer interface, with the substrate binding to one monomer and ATP to the, other. The overall fold of DTBS closely resembles that of three other, enzymes, adenylosuccinate synthetase (purA), Ha-ras-p21, and nitrogenase, iron protein, that are unrelated by sequence or function, indicating that, DTBS is a member of a diverse family of enzymes.
+<StructureSection load='1dbs' size='340' side='right'caption='[[1dbs]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dbs]] 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=1DBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBS FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1dbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbs OCA], [https://pdbe.org/1dbs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbs RCSB], [https://www.ebi.ac.uk/pdbsum/1dbs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbs 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/db/1dbs_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=1dbs ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-DBS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DBS OCA].
+*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Mechanistic implications and family relationships from the structure of dethiobiotin synthetase., Alexeev D, Baxter RL, Sawyer L, Structure. 1994 Nov 15;2(11):1061-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7881906 7881906]
+__TOC__
-[[Category: Dethiobiotin synthase]]
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Alexeev, D.]]
+[[Category: Alexeev D]]
-[[Category: Sawyer, L.]]
+[[Category: Sawyer L]]
-[[Category: SO4]]
-[[Category: biotin biosynthesis]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:08:45 2007''