2g09: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2g09]] 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=2G09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G09 FirstGlance]. <br> | <table><tr><td colspan='2'>[[2g09]] 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=2G09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G09 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PIN:PIPERAZINE-N,N-BIS(2-ETHANESULFONIC+ACID)'>PIN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PIN:PIPERAZINE-N,N-BIS(2-ETHANESULFONIC+ACID)'>PIN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]], [[2g0a|2g0a]]</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]], [[2g0a|2g0a]]</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=2g09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g09 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g09 RCSB], [http://www.ebi.ac.uk/pdbsum/2g09 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=2g09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g09 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g09 RCSB], [http://www.ebi.ac.uk/pdbsum/2g09 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]] | ||
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[[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: | [[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: Cesg]] | [[Category: Cesg]] | ||
[[Category: Cytosolic 5'-nucleotidase iii]] | [[Category: Cytosolic 5'-nucleotidase iii]] | ||
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[[Category: Nt5c3 protein]] | [[Category: Nt5c3 protein]] | ||
[[Category: P5n-1]] | [[Category: P5n-1]] | ||
[[Category: Protein structure initiative | [[Category: PSI, Protein structure initiative]] | ||
[[Category: Pyrimidine 5'-nucleotidase 1]] | [[Category: Pyrimidine 5'-nucleotidase 1]] | ||
[[Category: Umph-1]] | [[Category: Umph-1]] | ||
[[Category: Uniprot q9d020]] | [[Category: Uniprot q9d020]] | ||
Revision as of 22:32, 25 December 2014
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product complexX-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product complex
Structural highlights
Function[5NT3_MOUSE] Can act both as nucleotidase and as phosphotransferase (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedEukaryotic 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 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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