1pv9: Difference between revisions

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New page: left|200px<br /><applet load="1pv9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pv9, resolution 2.00Å" /> '''Prolidase from Pyroc...
 
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'''Prolidase from Pyrococcus furiosus'''<br />


==Overview==
==Prolidase from Pyrococcus furiosus==
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.
<StructureSection load='1pv9' size='340' side='right'caption='[[1pv9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
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 ZN 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].
</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>
 
<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>
==Reference==
<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>
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]
</table>
== Function ==
[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>
== 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/pv/1pv9_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/main_output.php?pdb_ID=1pv9 ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Single protein]]
[[Category: Adams MW]]
[[Category: Xaa-Pro dipeptidase]]
[[Category: Freeman HC]]
[[Category: Adams, M.W.]]
[[Category: Ghosh M]]
[[Category: Freeman, H.C.]]
[[Category: Grunden AM]]
[[Category: Ghosh, M.]]
[[Category: Guss JM]]
[[Category: Grunden, A.M.]]
[[Category: Maher MJ]]
[[Category: Guss, J.M.]]
[[Category: Menon AL]]
[[Category: Maher, M.J.]]
[[Category: Menon, A.L.]]
[[Category: ZN]]
[[Category: peptidase]]
[[Category: prolidase]]
[[Category: zinc]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:09:02 2007''

Latest revision as of 11:11, 14 February 2024

Prolidase from Pyrococcus furiosusProlidase from Pyrococcus furiosus

Structural highlights

1pv9 is a 2 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PEPQ_PYRFU Splits dipeptides with a prolyl in the C-terminal position and a nonpolar amino acid at the N-terminal position.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Ghosh M, Grunden AM, Dunn DM, Weiss R, Adams MW. Characterization of native and recombinant forms of an unusual cobalt-dependent proline dipeptidase (prolidase) from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 1998 Sep;180(18):4781-9. PMID:9733678

1pv9, resolution 2.00Å

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