2pz0

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{{Seed}}
 
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[[Image:2pz0.png|left|200px]]
 
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==Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis==
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The line below this paragraph, containing "STRUCTURE_2pz0", creates the "Structure Box" on the page.
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<StructureSection load='2pz0' size='340' side='right'caption='[[2pz0]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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<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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{{STRUCTURE_2pz0| PDB=2pz0 | SCENE= }}
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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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</table>
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== Function ==
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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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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18214974}}, adds the Publication Abstract to the page
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*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18214974 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18214974}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]]
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2PZ0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermoanaerobacter_tengcongensis_mb4 Thermoanaerobacter tengcongensis mb4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZ0 OCA].
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[[Category: Large Structures]]
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[[Category: An XM]]
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==Reference==
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[[Category: Liang DC]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18214974 18214974]
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[[Category: Liu JF]]
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[[Category: Single protein]]
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[[Category: Shi L]]
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[[Category: Thermoanaerobacter tengcongensis mb4]]
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[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
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[[Category: Glycerophosphodiester phosphodiesterase]]
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[[Category: Hydrolase]]
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[[Category: T. tengcongensis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 31 20:21:18 2008''
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Current revision

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

PDB ID 2pz0

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