1pv9

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[[Image:1pv9.jpg|left|200px]]<br /><applet load="1pv9" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pv9, resolution 2.00&Aring;" />
 
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'''Prolidase from Pyrococcus furiosus'''<br />
 
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==Overview==
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==Prolidase from Pyrococcus furiosus==
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The structure of prolidase from the hyperthermophilic archaeon Pyrococcus furiosus (Pfprol) has been solved and refined at 2.0 A resolution. This is the first structure of a prolidase, i.e., a peptidase specific for dipeptides having proline as the second residue. The asymmetric unit of the crystals contains a homodimer of the enzyme. Each of the two protein subunits has two domains. The C-terminal domain includes the catalytic site, which is centered on a dinuclear metal cluster. In the as-isolated form of Pfprol, the active-site metal atoms are Co(II) [Ghosh, M., et al. (1998) J. Bacteriol. 180, 4781-9]. An unexpected finding is that in the crystalline enzyme the active-site metal atoms are Zn(II), presumably as a result of metal exchange during crystallization. Both of the Zn(II) atoms are five-coordinate. The ligands include a bridging water molecule or hydroxide ion, which is likely to act as a nucleophile in the catalytic reaction. The two-domain polypeptide fold of Pfprol is similar to the folds of two functionally related enzymes, aminopeptidase P (APPro) and creatinase. In addition, the catalytic C-terminal domain of Pfprol has a polypeptide fold resembling that of the sole domain of a fourth enzyme, methionine aminopeptidase (MetAP). The active sites of APPro and MetAP, like that of Pfprol, include a dinuclear metal center. The metal ligands in the three enzymes are homologous. Comparisons with the molecular structures of APPro and MetAP suggest how Pfprol discriminates against oligopeptides and in favor of Xaa-Pro substrates. The crystal structure of Pfprol was solved by multiple-wavelength anomalous dispersion. The crystals yielded diffraction data of relatively high quality and resolution, despite the fact that one of the two protein subunits in the asymmetric unit was found to be significantly disordered. The final R and R(free) values are 0.24 and 0.28, respectively.
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<StructureSection load='1pv9' size='340' side='right'caption='[[1pv9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>
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1PV9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].
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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]] 2&#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=ZN:ZINC+ION'>ZN</scene></td></tr>
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==Reference==
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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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [https://pdbe.org/1pv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [https://www.ebi.ac.uk/pdbsum/1pv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pv9 ProSAT]</span></td></tr>
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Structure of the prolidase from Pyrococcus furiosus., Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC, Guss JM, Biochemistry. 2004 Mar 16;43(10):2771-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15005612 15005612]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PEPQ_PYRFU PEPQ_PYRFU] Splits dipeptides with a prolyl in the C-terminal position and a nonpolar amino acid at the N-terminal position.<ref>PMID:9733678</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/pv/1pv9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1pv9 ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Single protein]]
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[[Category: Adams MW]]
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[[Category: Xaa-Pro dipeptidase]]
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[[Category: Freeman HC]]
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[[Category: Adams, M W.]]
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[[Category: Ghosh M]]
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[[Category: Freeman, H C.]]
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[[Category: Grunden AM]]
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[[Category: Ghosh, M.]]
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[[Category: Guss JM]]
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[[Category: Grunden, A M.]]
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[[Category: Maher MJ]]
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[[Category: Guss, J M.]]
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[[Category: Menon AL]]
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[[Category: Maher, M J.]]
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[[Category: Menon, A L.]]
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[[Category: ZN]]
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[[Category: peptidase]]
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[[Category: prolidase]]
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[[Category: zinc]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:32:58 2008''
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Current revision

Prolidase from Pyrococcus furiosus

PDB ID 1pv9

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