2g0a - Revision history

OCA at 17:00, 11 September 2015

2015-09-11T17:00:09Z

←Older revision		Revision as of 17:00, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2g0a' size='340' side='right' caption='[[2g0a]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2g0a' size='340' side='right' caption='[[2g0a]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2g0a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2g0a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G0A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bdu\|2bdu]], [[2g06\|2g06]], [[2g07\|2g07]], [[2g08\|2g08]], [[2g09\|2g09]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bdu\|2bdu]], [[2g06\|2g06]], [[2g07\|2g07]], [[2g08\|2g08]], [[2g09\|2g09]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 ~~Mus musculus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </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=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB], [http://www.ebi.ac.uk/pdbsum/2g0a 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=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://pdbe.org/2g0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	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 2g0a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Lysophospholipase]]		[[Category: Lysophospholipase]]
-	[[Category: Mus musculus]]
	[[Category: Bingman, C A]]		[[Category: Bingman, C A]]
	[[Category: Bitto, E]]		[[Category: Bitto, E]]

OCA at 19:20, 25 December 2014

2014-12-25T19:20:02Z

←Older revision		Revision as of 19:20, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2g0a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G0A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2g0a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G0A FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bdu\|2bdu]], [[2g06\|2g06]], [[2g07\|2g07]], [[2g08\|2g08]], [[2g09\|2g09]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bdu\|2bdu]], [[2g06\|2g06]], [[2g07\|2g07]], [[2g08\|2g08]], [[2g09\|2g09]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </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=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB], [http://www.ebi.ac.uk/pdbsum/2g0a 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=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/5NT3_MOUSE 5NT3_MOUSE]] Can act both as nucleotidase and as phosphotransferase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Lysophospholipase]]		[[Category: Lysophospholipase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Bingman, C A.]]	+	[[Category: Bingman, C A]]
-	[[Category: Bitto, E.]]	+	[[Category: Bitto, E]]
-	[[Category: ~~CESG, Center for Eukaryotic~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Phillips, G N.]]	+	[[Category: Phillips, G N]]
-	[[Category: Wesenberg, G E.]]	+	[[Category: Wesenberg, G E]]
	[[Category: Aah38029]]		[[Category: Aah38029]]
	[[Category: Bc038029]]		[[Category: Bc038029]]
-	[[Category: Center for eukaryotic structural genomic]]
	[[Category: Cesg]]		[[Category: Cesg]]
	[[Category: Cytosolic 5'-nucleotidase iii]]		[[Category: Cytosolic 5'-nucleotidase iii]]
Line 49:		Line 50:
	[[Category: Nt5c3 protein]]		[[Category: Nt5c3 protein]]
	[[Category: P5n-1]]		[[Category: P5n-1]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi~~]]	+
	[[Category: Pyrimidine 5'-nucleotidase 1]]		[[Category: Pyrimidine 5'-nucleotidase 1]]
-	[[Category: Structural genomics functional follow-up study]]
	[[Category: Umph-1]]		[[Category: Umph-1]]
	[[Category: Uniprot q9d020]]		[[Category: Uniprot q9d020]]

OCA at 08:10, 30 September 2014

2014-09-30T08:10:07Z

←Older revision		Revision as of 08:10, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2g0a.~~png~~\|~~left~~\|200px]]	+	==X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site==
		+	<StructureSection load='2g0a' size='340' side='right' caption='[[2g0a]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2g0a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G0A FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bdu\|2bdu]], [[2g06\|2g06]], [[2g07\|2g07]], [[2g08\|2g08]], [[2g09\|2g09]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </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=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g0/2g0a_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Eukaryotic pyrimidine 5'-nucleotidase type 1 (P5N-1) catalyzes dephosphorylation of pyrimidine 5'-mononucleotides. Deficiency of P5N-1 activity in red blood cells results in nonspherocytic hemolytic anemia. The enzyme deficiency is either familial or can be acquired through lead poisoning. We present the crystal structure of mouse P5N-1 refined to 2.35 A resolution. The mouse P5N-1 has a 92% sequence identity to its human counterpart. The structure revealed that P5N-1 adopts a fold similar to enzymes of the haloacid dehydrogenase superfamily. The active site of this enzyme is structurally highly similar to those of phosphoserine phosphatases. We propose a catalytic mechanism for P5N-1 that is also similar to that of phosphoserine phosphatases and provide experimental evidence for the mechanism in the form of structures of several reaction cycle states, including: 1) P5N-1 with bound Mg(II) at 2.25 A, 2) phosphoenzyme intermediate analog at 2.30 A, 3) product-transition complex analog at 2.35 A, and 4) product complex at 2.1A resolution with phosphate bound in the active site. Furthermore the structure of Pb(II)-inhibited P5N-1 (at 2.35 A) revealed that Pb(II) binds within the active site in a way that compromises function of the cationic cavity, which is required for the recognition and binding of the phosphate group of nucleotides.

-	~~{{STRUCTURE_2g0a\| PDB=2g0a \| SCENE= }}~~	+	Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.,Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN Jr J Biol Chem. 2006 Jul 21;281(29):20521-9. Epub 2006 May 3. PMID:16672222<ref>PMID:16672222</ref>

-	~~===X-ray structure~~ of ~~mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16672222}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2g0a]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016672222<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Lysophospholipase]]		[[Category: Lysophospholipase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]

OCA: Protected "2g0a" [edit=sysop:move=sysop]

2013-01-07T10:37:07Z

Protected "2g0a" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:37, 7 January 2013

OCA at 10:37, 7 January 2013

2013-01-07T10:37:06Z

←Older revision		Revision as of 10:37, 7 January 2013
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-	{{Seed}}
	[[Image:2g0a.png\|left\|200px]]		[[Image:2g0a.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2g0a\| PDB=2g0a \| SCENE= }}		{{STRUCTURE_2g0a\| PDB=2g0a \| SCENE= }}

	===X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site===		===X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site===

-
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	{{ABSTRACT_PUBMED_16672222}}		{{ABSTRACT_PUBMED_16672222}}

	==About this Structure==		==About this Structure==
-	~~2G0A~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA].	+	[[2g0a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16672222~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016672222</ref><references group="xtra"/>
	[[Category: Lysophospholipase]]		[[Category: Lysophospholipase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
Line 29:		Line 17:
	[[Category: Bitto, E.]]		[[Category: Bitto, E.]]
	[[Category: CESG, Center for Eukaryotic Structural Genomics.]]		[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
-	[[Category: ~~Jr.~~, G N~~.Phillips~~.]]	+	[[Category: Phillips, G N.]]
	[[Category: Wesenberg, G E.]]		[[Category: Wesenberg, G E.]]
	[[Category: Aah38029]]		[[Category: Aah38029]]
Line 36:		Line 24:
	[[Category: Cesg]]		[[Category: Cesg]]
	[[Category: Cytosolic 5'-nucleotidase iii]]		[[Category: Cytosolic 5'-nucleotidase iii]]
		+	[[Category: Hydrolase]]
	[[Category: Lead poisoning]]		[[Category: Lead poisoning]]
	[[Category: Mm 158936]]		[[Category: Mm 158936]]
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	[[Category: Umph-1]]		[[Category: Umph-1]]
	[[Category: Uniprot q9d020]]		[[Category: Uniprot q9d020]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:18:06 2009''

OCA at 02:18, 18 February 2009

2009-02-18T02:18:08Z

←Older revision		Revision as of 02:18, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2G0A is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA].	+	2G0A is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G0A OCA].

	==Reference==		==Reference==
-	Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning., Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN Jr, J Biol Chem. 2006 Jul 21;281(29):20521-9. Epub 2006 May 3. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16672222 16672222]~~	+	<ref group="xtra">PMID:16672222</ref><references group="xtra"/>
	[[Category: Lysophospholipase]]		[[Category: Lysophospholipase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Single protein]]
	[[Category: Bingman, C A.]]		[[Category: Bingman, C A.]]
	[[Category: Bitto, E.]]		[[Category: Bitto, E.]]
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	[[Category: Uniprot q9d020]]		[[Category: Uniprot q9d020]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 10~~:55:~~23 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:18:06 2009''

OCA at 07:55, 29 July 2008

2008-07-29T07:55:25Z

←Older revision		Revision as of 07:55, 29 July 2008
Line 1:		Line 1:
-	[[Image:2g0a.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2g0a.png\|left\|200px]]

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	{{STRUCTURE_2g0a\| PDB=2g0a \| SCENE= }}		{{STRUCTURE_2g0a\| PDB=2g0a \| SCENE= }}

-	~~'''~~X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site~~'''~~	+	===X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site===


-	~~==Overview==~~	+	<!--
-	~~Eukaryotic pyrimidine 5'~~-~~nucleotidase type 1 (P5N~~-~~1) catalyzes dephosphorylation of pyrimidine 5'-mononucleotides. Deficiency of P5N-1 activity in red blood cells results in nonspherocytic hemolytic anemia.~~ The ~~enzyme deficiency is either familial or can be acquired through lead poisoning. We present~~ the ~~crystal structure of mouse P5N-1 refined to 2.35 A resolution. The mouse P5N-1 has a 92% sequence identity to its human counterpart. The structure revealed that P5N-1 adopts a fold similar~~ to ~~enzymes of~~ the haloacid dehydrogenase superfamily. The active site of this enzyme is structurally highly similar to those of phosphoserine phosphatases. We propose a catalytic mechanism for P5N-1 that is also similar to that of phosphoserine phosphatases and provide experimental evidence for the mechanism in the form of structures of several reaction cycle states, including: 1) P5N-1 with bound Mg(~~II)~~ at 2.~~25 A, 2) phosphoenzyme intermediate analog at 2~~.~~30 A, 3~~) ~~product-transition complex analog at 2.35 A~~, ~~and 4) product complex at 2.1A resolution with phosphate bound in~~ the ~~active site~~. ~~Furthermore the structure of Pb(II)~~-~~inhibited P5N~~-1 (at 2.35 A) revealed that Pb(II) binds within the active site in a way that compromises function of the cationic cavity, which is required for the recognition and binding of the phosphate group of nucleotides.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16672222}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16672222 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16672222}}

	==About this Structure==		==About this Structure==
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	[[Category: Umph-1]]		[[Category: Umph-1]]
	[[Category: Uniprot q9d020]]		[[Category: Uniprot q9d020]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 04~~:32:47 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 10:55:23 2008''

OCA at 01:32, 4 May 2008

2008-05-04T01:32:47Z

←Older revision		Revision as of 01:32, 4 May 2008
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	[[Image:2g0a.gif\|left\|200px]]		[[Image:2g0a.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 2g0a \|SIZE=350\|CAPTION= <scene name='initialview01'>2g0a</scene>~~, ~~resolution 2~~.~~350Å~~	+	The line below this paragraph, containing "STRUCTURE_2g0a", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=EPE:4-~~(~~2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</~~scene~~>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PB:LEAD+(II~~)~~+ION'>PB</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase]~~, ~~with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </span>~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= NT5C3 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])~~	+	-->
-	~~\|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG4359 COG4359], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam05822 UMPH~~-~~1]</span~~>	+	{{STRUCTURE_2g0a\| PDB=2g0a \| SCENE= }}
-	\|~~RELATEDENTRY~~=~~[[2bdu~~\|~~2BDU]], [[2g06\|2G06]], [[2g07\|2G07]], [[2g08\|2G08]], [[2g09\|2G09]]~~	+
-	~~\|RESOURCES~~=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB]</span>	+
-	}}	+

	'''X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site'''		'''X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site'''
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	[[Category: Jr., G N.Phillips.]]		[[Category: Jr., G N.Phillips.]]
	[[Category: Wesenberg, G E.]]		[[Category: Wesenberg, G E.]]
-	[[Category: ~~aah38029~~]]	+	[[Category: Aah38029]]
-	[[Category: ~~bc038029~~]]	+	[[Category: Bc038029]]
-	[[Category: ~~center~~ for eukaryotic structural genomic]]	+	[[Category: Center for eukaryotic structural genomic]]
-	[[Category: ~~cesg~~]]	+	[[Category: Cesg]]
-	[[Category: ~~cytosolic~~ 5'-nucleotidase iii]]	+	[[Category: Cytosolic 5'-nucleotidase iii]]
-	[[Category: ~~lead~~ poisoning]]	+	[[Category: Lead poisoning]]
-	[[Category: mm 158936]]	+	[[Category: Mm 158936]]
-	[[Category: ~~nt5c3~~ protein]]	+	[[Category: Nt5c3 protein]]
-	[[Category: ~~p5n~~-1]]	+	[[Category: P5n-1]]
-	[[Category: ~~protein~~ structure initiative]]	+	[[Category: Protein structure initiative]]
-	[[Category: ~~psi~~]]	+	[[Category: Psi]]
-	[[Category: ~~pyrimidine~~ 5'-nucleotidase 1]]	+	[[Category: Pyrimidine 5'-nucleotidase 1]]
-	[[Category: ~~structural~~ genomics functional follow-up study]]	+	[[Category: Structural genomics functional follow-up study]]
-	[[Category: ~~umph~~-1]]	+	[[Category: Umph-1]]
-	[[Category: ~~uniprot~~ q9d020]]	+	[[Category: Uniprot q9d020]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 04:32:47 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 03~~:10:06 2008''	+

OCA at 00:10, 31 March 2008

2008-03-31T00:10:09Z

←Older revision		Revision as of 00:10, 31 March 2008
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	\|GENE= NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])		\|GENE= NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
	\|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG4359 COG4359], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam05822 UMPH-1]</span>		\|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG4359 COG4359], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam05822 UMPH-1]</span>
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum~~], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib~~], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB]</span>	+	\|RELATEDENTRY=[[2bdu\|2BDU]], [[2g06\|2G06]], [[2g07\|2G07]], [[2g08\|2G08]], [[2g09\|2G09]]
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB]</span>
	}}		}}

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	[[Category: uniprot q9d020]]		[[Category: uniprot q9d020]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed~~ Mar ~~26 06~~:25:49 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:10:06 2008''

OCA at 04:25, 26 March 2008

2008-03-26T04:25:50Z

←Older revision		Revision as of 04:25, 26 March 2008
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	\|PDB= 2g0a \|SIZE=350\|CAPTION= <scene name='initialview01'>2g0a</scene>, resolution 2.350Å		\|PDB= 2g0a \|SIZE=350\|CAPTION= <scene name='initialview01'>2g0a</scene>, resolution 2.350Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=PB:~~LEAD+~~(II)+~~ION~~'>PB</scene> ~~and~~ <scene name='pdbligand=~~EPE~~:4-(~~2-HYDROXYETHYL~~)~~-1-PIPERAZINE ETHANESULFONIC ACID~~'>~~EPE~~</scene>	+	\|LIGAND= <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene>
-	\|ACTIVITY= [http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5]	+	\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysophospholipase Lysophospholipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.5 3.1.1.5] </span>
	\|GENE= NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])		\|GENE= NT5C3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
		+	\|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG4359 COG4359], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam05822 UMPH-1]</span>
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g0a OCA], [http://www.ebi.ac.uk/pdbsum/2g0a PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2g0a RCSB]</span>
	}}		}}

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	[[Category: Jr., G N.Phillips.]]		[[Category: Jr., G N.Phillips.]]
	[[Category: Wesenberg, G E.]]		[[Category: Wesenberg, G E.]]
-	[[Category: EPE]]
-	[[Category: PB]]
	[[Category: aah38029]]		[[Category: aah38029]]
	[[Category: bc038029]]		[[Category: bc038029]]
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	[[Category: uniprot q9d020]]		[[Category: uniprot q9d020]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 16~~:58:53 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:25:49 2008''