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3qy0

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Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP

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 ==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP==
-<StructureSection load='3qy0' size='340' side='right' caption='[[3qy0]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='3qy0' size='340' side='right'caption='[[3qy0]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3qy0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QY0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QY0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3qy0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QY0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qmo|2qmo]], [[3mle|3mle]], [[3qxc|3qxc]], [[3qxh|3qxh]], [[3qxj|3qxj]], [[3qxs|3qxs]], [[3qxx|3qxx]]</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>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bioD, hp0029, HP_0029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Helicobacter pylori 26695])</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=3qy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qy0 OCA], [https://pdbe.org/3qy0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qy0 RCSB], [https://www.ebi.ac.uk/pdbsum/3qy0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qy0 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<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=3qy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qy0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qy0 RCSB], [http://www.ebi.ac.uk/pdbsum/3qy0 PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/BIOD_HELPY BIOD_HELPY] 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 (By similarity).[HAMAP-Rule:MF_00336]
-Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS.ATP and hpDTBS.GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway. Database Coordinates and structure factors for structures presented in this article have been deposited in the Protein Data Bank under the following accession codes: 2QMO - apo-form; 3MLE - hpDTBS.8-ac.ADP. in P2(1) 2(1) 2(1) form; 3QXC - hpDTBS.ATP; 3QXH - hpDTBS.8-ac:ADP. in C2 form; 3QXJ - hpDTBS.GTP; 3QXS - hpDTBS.ANP; 3QXX - 8-ac.GDP.; and 3QY0 - hpDTBS.GDP.. Structured digital abstract * hpDTBS and hpDTBS bind by x-ray crystallography (View interaction).
-Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.,Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W FEBS J. 2012 Jan 27. doi: 10.1111/j.1742-4658.2012.08506.x. PMID:22284390<ref>PMID:22284390</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Dethiobiotin synthetase|Dethiobiotin synthetase]]
+*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Dethiobiotin synthase]]
 [[Category: Helicobacter pylori 26695]]
-[[Category: Chruszcz, M]]
+[[Category: Large Structures]]
-[[Category: Joachimiak, A]]
+[[Category: Chruszcz M]]
-[[Category: Klimecka, M M]]
+[[Category: Joachimiak A]]
-[[Category: Structural genomic]]
+[[Category: Klimecka MM]]
-[[Category: Minor, W]]
+[[Category: Minor W]]
-[[Category: Murzyn, K]]
+[[Category: Murzyn K]]
-[[Category: Porebski, P J]]
+[[Category: Porebski PJ]]
-[[Category: Dethiobiotin synthetase]]
-[[Category: Dtb]]
-[[Category: Ligase]]
-[[Category: Mcsg]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Psi-biology]]

3qy0

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Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP

Structural highlights

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