2pz0

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(New page: 200px {{Structure |PDB= 2pz0 |SIZE=350|CAPTION= <scene name='initialview01'>2pz0</scene>, resolution 1.91&Aring; |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+F...)
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[[Image:2pz0.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis==
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|PDB= 2pz0 |SIZE=350|CAPTION= <scene name='initialview01'>2pz0</scene>, resolution 1.91&Aring;
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<StructureSection load='2pz0' size='340' side='right'caption='[[2pz0]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+501'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+B+502'>AC2</scene>, <scene name='pdbsite=AC3:Gol+Binding+Site+For+Residue+B+400'>AC3</scene> and <scene name='pdbsite=AC4:Gol+Binding+Site+For+Residue+A+401'>AC4</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[2pz0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PZ0 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.91&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0584 UgpQ], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03009 GDPD]</span>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pz0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pz0 OCA], [https://pdbe.org/2pz0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pz0 RCSB], [https://www.ebi.ac.uk/pdbsum/2pz0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pz0 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pz0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pz0 OCA], [http://www.ebi.ac.uk/pdbsum/2pz0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pz0 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GDPD_CALS4 GDPD_CALS4] Glycerophosphodiester phosphodiesterase hydrolyzes glycerophosphodiesters into glycerol-3-phosphate (G3P) and the corresponding alcohol (PubMed:18214974). Can use glycerophosphocholine (PubMed:18214974).<ref>PMID:18214974</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pz/2pz0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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/main_output.php?pdb_ID=2pz0 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Glycerophosphodiester phosphodiesterase (GDPD; EC 3.1.4.46) catalyzes the hydrolysis of a glycerophosphodiester to an alcohol and glycerol 3-phosphate in glycerol metabolism. It has an important role in the synthesis of a variety of products that participate in many biochemical pathways. We report the crystal structure of the Thermoanaerobacter tengcongensis GDPD (ttGDPD) at 1.91 A resolution, with a calcium ion and glycerol as a substrate mimic coordinated at this calcium ion (PDB entry 2pz0). The ttGDPD dimer with an intermolecular disulfide bridge and two hydrogen bonds is considered as the potential functional unit. We used site-directed mutagenesis to characterize ttGDPD as a metal ion-dependent enzyme, identified a cluster of residues involved in substrate binding and the catalytic reaction, and we propose a possible general acid-base catalytic mechanism for ttGDPD. Superposing the active site with the homologous structure GDPD from Agrobacterium tumefaciens (PDB entry 1zcc), which binds a sulfate ion in the active site, the sulfate ion can represent the phosphate moiety of the substrate, simulating the binding mode of the true substrate of GDPD.
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'''Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis'''
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Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.,Shi L, Liu JF, An XM, Liang DC Proteins. 2008 Jul;72(1):280-8. PMID:18214974<ref>PMID:18214974</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2pz0" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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2PZ0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermoanaerobacter_tengcongensis Thermoanaerobacter tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZ0 OCA].
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*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
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[[Category: Single protein]]
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== References ==
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[[Category: Thermoanaerobacter tengcongensis]]
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<references/>
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[[Category: An, X M.]]
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__TOC__
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[[Category: Liang, D C.]]
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</StructureSection>
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[[Category: Liu, J F.]]
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[[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]]
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[[Category: Shi, L.]]
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[[Category: Large Structures]]
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[[Category: glycerophosphodiester phosphodiesterase]]
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[[Category: An XM]]
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[[Category: hydrolase]]
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[[Category: Liang DC]]
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[[Category: t. tengcongensis]]
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[[Category: Liu JF]]
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[[Category: Shi L]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:58:03 2008''
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Current revision

Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis

PDB ID 2pz0

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