4d8v - Revision history

OCA at 10:42, 1 March 2024

OCA — Fri, 01 Mar 2024 10:42:49 GMT

←Older revision		Revision as of 10:42, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [https://pdbe.org/4d8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [https://www.ebi.ac.uk/pdbsum/4d8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8v 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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [https://pdbe.org/4d8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [https://www.ebi.ac.uk/pdbsum/4d8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU]] Cleavage of adenosine and its derivatives.	+	[https://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU] Cleavage of adenosine and its derivatives.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl(6) and Br(8) substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.	+
-		+
-	Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.,de Giuseppe PO, Martins NH, Meza AN, Dos Santos CR, Pereira HD, Murakami MT PLoS One. 2012;7(9):e44282. Epub 2012 Sep 5. PMID:22957058<ref>PMID:22957058</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4d8v" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]		*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:52, 14 September 2022

OCA — Wed, 14 Sep 2022 07:52:54 GMT

←Older revision		Revision as of 07:52, 14 September 2022
Line 1:		Line 1:

	==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2==		==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2==
-	<StructureSection load='4d8v' size='340' side='right' caption='[[4d8v]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='4d8v' size='340' side='right'caption='[[4d8v]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d8x\|4d8x]], [[4d8y\|4d8y]], [[4d98\|4d98]], [[4d9h\|4d9h]], [[4da0\|4da0]], [[4da6\|4da6]], [[4da7\|4da7]], [[4da8\|4da8]], [[4dab\|4dab]], [[4dae\|4dae]], [[4dan\|4dan]], [[4dao\|4dao]], [[4dar\|4dar]]</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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [https://pdbe.org/4d8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [https://www.ebi.ac.uk/pdbsum/4d8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8v ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [~~http~~://pdbe.org/4d8v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d8v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU]] Cleavage of adenosine and its derivatives.	+	[[https://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU]] Cleavage of adenosine and its derivatives.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==See Also==		==See Also==
-	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]	+	*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~globigii migula 1900~~]]	+	[[Category: Bacillus subtilis]]
-	[[Category: ~~Purine-nucleoside phosphorylase~~]]	+	[[Category: Large Structures]]
-	[[Category: Giuseppe~~, P O~~]]	+	[[Category: Giuseppe PO]]
-	[[Category: Martins~~, N H~~]]	+	[[Category: Martins NH]]
-	[[Category: Meza~~, A N~~]]	+	[[Category: Meza AN]]
-	[[Category: Murakami~~, M T~~]]	+	[[Category: Murakami MT]]
-	[[Category: Santos~~, C R]]~~	+	[[Category: Santos CR]]
-	~~[[Category: Phosphorylase/hydrolase-like]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 16:00, 11 August 2016

OCA — Thu, 11 Aug 2016 16:00:52 GMT

←Older revision		Revision as of 16:00, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2==		==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2==
	<StructureSection load='4d8v' size='340' side='right' caption='[[4d8v]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='4d8v' size='340' side='right' caption='[[4d8v]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d8x\|4d8x]], [[4d8y\|4d8y]], [[4d98\|4d98]], [[4d9h\|4d9h]], [[4da0\|4da0]], [[4da6\|4da6]], [[4da7\|4da7]], [[4da8\|4da8]], [[4dab\|4dab]], [[4dae\|4dae]], [[4dan\|4dan]], [[4dao\|4dao]], [[4dar\|4dar]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d8x\|4d8x]], [[4d8y\|4d8y]], [[4d98\|4d98]], [[4d9h\|4d9h]], [[4da0\|4da0]], [[4da6\|4da6]], [[4da7\|4da7]], [[4da8\|4da8]], [[4dab\|4dab]], [[4dae\|4dae]], [[4dan\|4dan]], [[4dao\|4dao]], [[4dar\|4dar]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [http://www.ebi.ac.uk/pdbsum/4d8v 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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [http://pdbe.org/4d8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [http://www.ebi.ac.uk/pdbsum/4d8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU]] Cleavage of adenosine and its derivatives.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		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 4d8v" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Giuseppe, P O]]		[[Category: Giuseppe, P O]]

OCA at 12:27, 4 January 2015

OCA — Sun, 04 Jan 2015 12:27:40 GMT

←Older revision		Revision as of 12:27, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d8x\|4d8x]], [[4d8y\|4d8y]], [[4d98\|4d98]], [[4d9h\|4d9h]], [[4da0\|4da0]], [[4da6\|4da6]], [[4da7\|4da7]], [[4da8\|4da8]], [[4dab\|4dab]], [[4dae\|4dae]], [[4dan\|4dan]], [[4dao\|4dao]], [[4dar\|4dar]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d8x\|4d8x]], [[4d8y\|4d8y]], [[4d98\|4d98]], [[4d9h\|4d9h]], [[4da0\|4da0]], [[4da6\|4da6]], [[4da7\|4da7]], [[4da8\|4da8]], [[4dab\|4dab]], [[4dae\|4dae]], [[4dan\|4dan]], [[4dao\|4dao]], [[4dar\|4dar]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [http://www.ebi.ac.uk/pdbsum/4d8v 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=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [http://www.ebi.ac.uk/pdbsum/4d8v PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
-	[[Category: Giuseppe, P O.]]	+	[[Category: Giuseppe, P O]]
-	[[Category: Martins, N H.]]	+	[[Category: Martins, N H]]
-	[[Category: Meza, A N.]]	+	[[Category: Meza, A N]]
-	[[Category: Murakami, M T.]]	+	[[Category: Murakami, M T]]
-	[[Category: Santos, C R.]]	+	[[Category: Santos, C R]]
	[[Category: Phosphorylase/hydrolase-like]]		[[Category: Phosphorylase/hydrolase-like]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:11, 2 July 2014

OCA — Wed, 02 Jul 2014 09:11:33 GMT

←Older revision		Revision as of 09:11, 2 July 2014
Line 1:		Line 1:
-	[[~~Image:~~4d8v.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2==
		+	<StructureSection load='4d8v' size='340' side='right' caption='[[4d8v]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4d8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d8x\|4d8x]], [[4d8y\|4d8y]], [[4d98\|4d98]], [[4d9h\|4d9h]], [[4da0\|4da0]], [[4da6\|4da6]], [[4da7\|4da7]], [[4da8\|4da8]], [[4dab\|4dab]], [[4dae\|4dae]], [[4dan\|4dan]], [[4dao\|4dao]], [[4dar\|4dar]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d8v RCSB], [http://www.ebi.ac.uk/pdbsum/4d8v PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl(6) and Br(8) substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.

-	~~{{STRUCTURE_4d8v\| PDB=4d8v \| SCENE= }}~~	+	Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.,de Giuseppe PO, Martins NH, Meza AN, Dos Santos CR, Pereira HD, Murakami MT PLoS One. 2012;7(9):e44282. Epub 2012 Sep 5. PMID:22957058<ref>PMID:22957058</ref>

-	~~===Crystal structure~~ of the ~~hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4~~.~~2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22957058}}~~	+	==See Also==
-		+	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4d8v~~]] ~~is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA].~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]

OCA at 20:39, 26 September 2012

OCA — Wed, 26 Sep 2012 20:39:16 GMT

←Older revision		Revision as of 20:39, 26 September 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4d8v.jpg\|left\|200px]]

-	~~The entry~~ 4d8v ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4d8v\| PDB=4d8v \| SCENE= }}

-	~~Authors: Santos, C.R., Meza, A.N., Martins, N.H., Giuseppe, P.O., Murakami, M.T~~.	+	===Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2===

-	~~Description: Crystal~~ structure ~~of the hexameric purine nucleoside phosphorylase~~ from Bacillus subtilis ~~at pH 4~~.2	+	{{ABSTRACT_PUBMED_22957058}}
		+
		+	==About this Structure==
		+	[[4d8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8V OCA].
		+	[[Category: Bacillus subtilis]]
		+	[[Category: Purine-nucleoside phosphorylase]]
		+	[[Category: Giuseppe, P O.]]
		+	[[Category: Martins, N H.]]
		+	[[Category: Meza, A N.]]
		+	[[Category: Murakami, M T.]]
		+	[[Category: Santos, C R.]]
		+	[[Category: Phosphorylase/hydrolase-like]]
		+	[[Category: Transferase]]

OCA at 06:08, 14 March 2012

OCA — Wed, 14 Mar 2012 06:08:59 GMT

←Older revision		Revision as of 06:08, 14 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4d8v is ON HOLD	+	The entry 4d8v is ON HOLD until Paper Publication

	Authors: Santos, C.R., Meza, A.N., Martins, N.H., Giuseppe, P.O., Murakami, M.T.		Authors: Santos, C.R., Meza, A.N., Martins, N.H., Giuseppe, P.O., Murakami, M.T.

	Description: Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2		Description: Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2

OCA: Protected "4d8v" [edit=sysop:move=sysop]

OCA — Wed, 18 Jan 2012 10:27:05 GMT

Protected "4d8v" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:27, 18 January 2012

OCA: New page: '''Unreleased structure''' The entry 4d8v is ON HOLD Authors: Santos, C.R., Meza, A.N., Martins, N.H., Giuseppe, P.O., Murakami, M.T. Description: Crystal structure of the hexameric pu...

OCA — Wed, 18 Jan 2012 10:27:04 GMT

New page: '''Unreleased structure''' The entry 4d8v is ON HOLD Authors: Santos, C.R., Meza, A.N., Martins, N.H., Giuseppe, P.O., Murakami, M.T. Description: Crystal structure of the hexameric pu...

New page

'''Unreleased structure'''

The entry 4d8v is ON HOLD

Authors: Santos, C.R., Meza, A.N., Martins, N.H., Giuseppe, P.O., Murakami, M.T.

Description: Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2