3qxj - Revision history

OCA at 12:02, 14 March 2024

OCA — Thu, 14 Mar 2024 12:02:24 GMT

←Older revision		Revision as of 12:02, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[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]		[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]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3qxj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dethiobiotin synthetase 3D structures\|Dethiobiotin synthetase 3D structures]]		*[[Dethiobiotin synthetase 3D structures\|Dethiobiotin synthetase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:46, 17 January 2024

OCA — Wed, 17 Jan 2024 12:46:28 GMT

←Older revision		Revision as of 12:46, 17 January 2024
Line 3:		Line 3:
	<StructureSection load='3qxj' size='340' side='right'caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>		<StructureSection load='3qxj' size='340' side='right'caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxj]] 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=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXJ FirstGlance]. <br>
-	</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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.38Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2qmo\|2qmo]], [[3mle\|3mle]], [[3qxc\|3qxc]], [[3qxh\|3qxh]], [[3qxs\|3qxs]], [[3qxx\|3qxx]], [[3qy0\|3qy0]]~~</~~div~~><~~/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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~bioD~~, ~~hp0029, HP_0029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [https://pdbe.org/3qxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [https://www.ebi.ac.uk/pdbsum/3qxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxj ProSAT]</span></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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [https://pdbe.org/3qxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [https://www.ebi.ac.uk/pdbsum/3qxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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]	+	[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
-	~~[[Category: Dethiobiotin synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chruszcz, M]]	+	[[Category: Chruszcz M]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	[[Category: Klimecka~~, M M]]~~	+	[[Category: Klimecka MM]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Minor W]]
-	[[Category: Minor, W]]	+	[[Category: Murzyn K]]
-	[[Category: Murzyn, K]]	+	[[Category: Porebski PJ]]
-	[[Category: Porebski~~, P J]]~~	+
-	~~[[Category: Adp binding]]~~	+
-	~~[[Category: Dethiobiotin synthetase]]~~	+
-	~~[[Category: Dtb]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Psi-biology~~]]	+

OCA at 09:57, 13 April 2022

OCA — Wed, 13 Apr 2022 09:57:31 GMT

←Older revision		Revision as of 09:57, 13 April 2022
Line 1:		Line 1:

	==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP==		==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP==
-	<StructureSection load='3qxj' size='340' side='right' caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>	+	<StructureSection load='3qxj' size='340' side='right'caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXJ 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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>	+	</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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></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]], [[3qxs\|3qxs]], [[3qxx\|3qxx]], [[3qy0\|3qy0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qmo\|2qmo]], [[3mle\|3mle]], [[3qxc\|3qxc]], [[3qxh\|3qxh]], [[3qxs\|3qxs]], [[3qxx\|3qxx]], [[3qy0\|3qy0]]</div></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 Campylobacter pylori])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bioD, hp0029, HP_0029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [https://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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [~~http~~://pdbe.org/3qxj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qxj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxj ProSAT]</span></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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [https://pdbe.org/3qxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [https://www.ebi.ac.uk/pdbsum/3qxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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]	+	[[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]	+	*[[Dethiobiotin synthetase 3D structures\|Dethiobiotin synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	[[Category: Campylobacter pylori]]		[[Category: Campylobacter pylori]]
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
		+	[[Category: Large Structures]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 19:09, 4 August 2016

OCA — Thu, 04 Aug 2016 19:09:06 GMT

←Older revision		Revision as of 19:09, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP==		==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP==
	<StructureSection load='3qxj' size='340' side='right' caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>		<StructureSection load='3qxj' size='340' side='right' caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxj]] 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=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXJ 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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></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]], [[3qxs\|3qxs]], [[3qxx\|3qxx]], [[3qy0\|3qy0]]</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]], [[3qxs\|3qxs]], [[3qxx\|3qxx]], [[3qy0\|3qy0]]</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='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 Campylobacter pylori])</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='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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [http://www.ebi.ac.uk/pdbsum/3qxj PDBsum]</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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [http://pdbe.org/3qxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [http://www.ebi.ac.uk/pdbsum/3qxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3qxj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori]]
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
-	[[Category: Helicobacter pylori 26695]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 18:33, 24 December 2014

OCA — Wed, 24 Dec 2014 18:33:49 GMT

←Older revision		Revision as of 18:33, 24 December 2014
Line 9:		Line 9:
	<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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [http://www.ebi.ac.uk/pdbsum/3qxj PDBsum]</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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [http://www.ebi.ac.uk/pdbsum/3qxj PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:15, 19 December 2014

OCA — Fri, 19 Dec 2014 10:15:09 GMT

←Older revision		Revision as of 10:15, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3qxj\| PDB=3qxj \| SCENE= }}~~	+	==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP==
-	===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP===	+	<StructureSection load='3qxj' size='340' side='right' caption='[[3qxj]], [[Resolution\|resolution]] 1.38Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22284390}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qxj]] 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=3QXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXJ 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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></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]], [[3qxs\|3qxs]], [[3qxx\|3qxx]], [[3qy0\|3qy0]]</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='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=3qxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxj RCSB], [http://www.ebi.ac.uk/pdbsum/3qxj PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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).

-	~~==Function==~~	+	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>
-	~~[[http://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]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3qxj]] 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=3QXJ OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]		*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:022284390</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Helicobacter pylori 26695]]		[[Category: Helicobacter pylori 26695]]
-	[[Category: Chruszcz, M.]]	+	[[Category: Chruszcz, M]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: Klimecka, M M.]]	+	[[Category: Klimecka, M M]]
-	[[Category: ~~MCSG, Midwest Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Minor, W.]]	+	[[Category: Minor, W]]
-	[[Category: Murzyn, K.]]	+	[[Category: Murzyn, K]]
-	[[Category: Porebski, P J.]]	+	[[Category: Porebski, P J]]
	[[Category: Adp binding]]		[[Category: Adp binding]]
	[[Category: Dethiobiotin synthetase]]		[[Category: Dethiobiotin synthetase]]
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	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Mcsg]]		[[Category: Mcsg]]
-	[[Category: ~~Midwest center for structural genomic]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
-	[[Category: Structural genomic]]

OCA at 07:42, 27 March 2013

OCA — Wed, 27 Mar 2013 07:42:15 GMT

←Older revision		Revision as of 07:42, 27 March 2013
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-	[[Image:3qxj.png\|left\|200px]]
-
	{{STRUCTURE_3qxj\| PDB=3qxj \| SCENE= }}		{{STRUCTURE_3qxj\| PDB=3qxj \| SCENE= }}
-
	===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP===		===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP===
		+	{{ABSTRACT_PUBMED_22284390}}

-	~~{{ABSTRACT_PUBMED_22284390}}~~	+	==Function==
		+	[[http://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]

	==About this Structure==		==About this Structure==
-	[[3qxj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori~~ Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].	+	[[3qxj]] 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=3QXJ OCA].

	==See Also==		==See Also==
Line 14:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022284390</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022284390</ref><references group="xtra"/><references/>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
-	[[Category: Helicobacter pylori]]	+	[[Category: Helicobacter pylori 26695]]
	[[Category: Chruszcz, M.]]		[[Category: Chruszcz, M.]]
	[[Category: Joachimiak, A.]]		[[Category: Joachimiak, A.]]

OCA at 08:00, 20 October 2012

OCA — Sat, 20 Oct 2012 08:00:45 GMT

←Older revision		Revision as of 08:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3qxj]] is a 1 chain structure ~~of [[Dethiobiotin synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].	+	[[3qxj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].

	==See Also==		==See Also==

OCA at 18:10, 25 July 2012

OCA — Wed, 25 Jul 2012 18:10:02 GMT

←Older revision		Revision as of 18:10, 25 July 2012
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	[[Image:3qxj.png\|left\|200px]]		[[Image:3qxj.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_3qxj\| PDB=3qxj \| SCENE= }}		{{STRUCTURE_3qxj\| PDB=3qxj \| SCENE= }}

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

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22284390}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22284390 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22284390}}		{{ABSTRACT_PUBMED_22284390}}

	==About this Structure==		==About this Structure==
-	[[3qxj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].	+	[[3qxj]] is a 1 chain structure of [[Dethiobiotin synthetase]] with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].
		+
		+	==See Also==
		+	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]

	==Reference==		==Reference==

OCA at 06:30, 28 March 2012

OCA — Wed, 28 Mar 2012 06:30:53 GMT

←Older revision		Revision as of 06:30, 28 March 2012
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-	[[Image:3qxj.~~jpg~~\|left\|200px]]	+	[[Image:3qxj.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP===		===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22284390}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22284390 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22284390}}

	==About this Structure==		==About this Structure==
	[[3qxj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].		[[3qxj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXJ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022284390</ref><references group="xtra"/>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
Line 23:		Line 32:
	[[Category: Murzyn, K.]]		[[Category: Murzyn, K.]]
	[[Category: Porebski, P J.]]		[[Category: Porebski, P J.]]
		+	[[Category: Adp binding]]
		+	[[Category: Dethiobiotin synthetase]]
		+	[[Category: Dtb]]
		+	[[Category: Ligase]]
		+	[[Category: Mcsg]]
		+	[[Category: Midwest center for structural genomic]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-biology]]
		+	[[Category: Structural genomic]]