3qxs - Revision history

OCA at 12:02, 14 March 2024

2024-03-14T12:02:36Z

←Older revision		Revision as of 12:02, 14 March 2024
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	== 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 3qxs" 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

2024-01-17T12:46:30Z

←Older revision		Revision as of 12:46, 17 January 2024
Line 3:		Line 3:
	<StructureSection load='3qxs' size='340' side='right'caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='3qxs' size='340' side='right'caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.35Å</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]], [[3qxj\|3qxj]], [[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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [https://pdbe.org/3qxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [https://www.ebi.ac.uk/pdbsum/3qxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxs 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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [https://pdbe.org/3qxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [https://www.ebi.ac.uk/pdbsum/3qxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxs 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 ==
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	__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: Jablonska, K]]	+	[[Category: Jablonska K]]
-	[[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: Dethiobiotin synthetase]]~~	+
-	~~[[Category: Dtb]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Psi-biology~~]]	+

OCA at 09:57, 13 April 2022

2022-04-13T09:57:35Z

←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 ANP==		==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP==
-	<StructureSection load='3qxs' size='340' side='right' caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>	+	<StructureSection load='3qxs' size='340' side='right'caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]], [[3qxj\|3qxj]], [[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]], [[3qxj\|3qxj]], [[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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [~~http~~://pdbe.org/3qxs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qxs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxs 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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [https://pdbe.org/3qxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [https://www.ebi.ac.uk/pdbsum/3qxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxs 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: Jablonska, K]]		[[Category: Jablonska, K]]

OCA at 16:49, 4 August 2016

2016-08-04T16:49:18Z

←Older revision		Revision as of 16:49, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP==		==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP==
	<StructureSection load='3qxs' size='340' side='right' caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='3qxs' size='340' side='right' caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]], [[3qxj\|3qxj]], [[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]], [[3qxj\|3qxj]], [[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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [http://www.ebi.ac.uk/pdbsum/3qxs 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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [http://pdbe.org/3qxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [http://www.ebi.ac.uk/pdbsum/3qxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxs 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 3qxs" 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: Jablonska, K]]		[[Category: Jablonska, K]]

OCA at 11:07, 25 December 2014

2014-12-25T11:07:05Z

←Older revision		Revision as of 11:07, 25 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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [http://www.ebi.ac.uk/pdbsum/3qxs 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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [http://www.ebi.ac.uk/pdbsum/3qxs 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 11:11, 19 December 2014

2014-12-19T11:11:04Z

←Older revision		Revision as of 11:11, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3qxs\| PDB=3qxs \| SCENE= }}~~	+	==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP==
-	===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP===	+	<StructureSection load='3qxs' size='340' side='right' caption='[[3qxs]], [[Resolution\|resolution]] 1.35Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22284390}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qxs]] 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=3QXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]], [[3qxj\|3qxj]], [[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=3qxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxs RCSB], [http://www.ebi.ac.uk/pdbsum/3qxs 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>
-	~~[[3qxs]] 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=3QXS OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]		*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]
-	*[[Thrombin\|Thrombin]]	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	~~<ref group="xtra">PMID:022284390</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</StructureSection>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Helicobacter pylori 26695]]		[[Category: Helicobacter pylori 26695]]
-	[[Category: Chruszcz, M.]]	+	[[Category: Chruszcz, M]]
-	[[Category: Jablonska, K.]]	+	[[Category: Jablonska, K]]
-	[[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: Dethiobiotin synthetase]]		[[Category: Dethiobiotin synthetase]]
	[[Category: Dtb]]		[[Category: Dtb]]
	[[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 07:55, 27 March 2013

2013-03-27T07:55:48Z

←Older revision		Revision as of 07:55, 27 March 2013
Line 1:		Line 1:
-	[[Image:3qxs.png\|left\|200px]]
-
	{{STRUCTURE_3qxs\| PDB=3qxs \| SCENE= }}		{{STRUCTURE_3qxs\| PDB=3qxs \| SCENE= }}
-
	===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP===		===Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP===
		+	{{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==
-	[[3qxs]] 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=3QXS OCA].	+	[[3qxs]] 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=3QXS OCA].

	==See Also==		==See Also==
Line 15:		Line 14:

	==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: Jablonska, K.]]		[[Category: Jablonska, K.]]

OCA at 15:59, 20 October 2012

2012-10-20T15:59:26Z

←Older revision		Revision as of 15:59, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3qxs]] is a 1 chain structure ~~of [[Dethiobiotin synthetase]] and [[Thrombin]]~~ 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=3QXS OCA].	+	[[3qxs]] 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=3QXS OCA].

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

OCA at 20:14, 26 July 2012

2012-07-26T20:14:05Z

←Older revision		Revision as of 20:14, 26 July 2012
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	[[Image:3qxs.png\|left\|200px]]		[[Image:3qxs.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3qxs\| PDB=3qxs \| SCENE= }}		{{STRUCTURE_3qxs\| PDB=3qxs \| SCENE= }}

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

-
-	<!--
-	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.
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	{{ABSTRACT_PUBMED_22284390}}		{{ABSTRACT_PUBMED_22284390}}

	==About this Structure==		==About this Structure==
-	[[3qxs]] 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=3QXS OCA].	+	[[3qxs]] is a 1 chain structure of [[Dethiobiotin synthetase]] and [[Thrombin]] 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=3QXS OCA].
		+
		+	==See Also==
		+	*[[Dethiobiotin synthetase\|Dethiobiotin synthetase]]
		+	*[[Thrombin\|Thrombin]]

	==Reference==		==Reference==

OCA at 07:04, 28 March 2012

2012-03-28T07:04:24Z

←Older revision		Revision as of 07:04, 28 March 2012
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-	[[Image:3qxs.~~jpg~~\|left\|200px]]	+	[[Image:3qxs.png\|left\|200px]]

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

		+
		+	<!--
		+	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==
	[[3qxs]] 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=3QXS OCA].		[[3qxs]] 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=3QXS OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022284390</ref><references group="xtra"/>
	[[Category: Dethiobiotin synthase]]		[[Category: Dethiobiotin synthase]]
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
Line 24:		Line 33:
	[[Category: Murzyn, K.]]		[[Category: Murzyn, K.]]
	[[Category: Porebski, P J.]]		[[Category: Porebski, P J.]]
		+	[[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]]