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New page: left|200px<br /><applet load="1wm1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wm1, resolution 2.1Å" /> '''Crystal Structure of ...
 
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[[Image:1wm1.jpg|left|200px]]<br /><applet load="1wm1" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1wm1, resolution 2.1&Aring;" />
'''Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA'''<br />


==Overview==
==Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA==
Prolyl aminopeptidase from Serratia marcescens hydrolyzed, x-beta-naphthylamides (x=prolyl, alanyl, sarcosinyl, L-alpha-aminobutylyl, and norvalyl), which suggested that the enzyme has a pocket for a, five-member ring. Based on the substrate specificity, novel inhibitors of, Pro, Ala, and Sar having 2-tert-butyl-[1,3,4]oxadiazole (TBODA) were, synthesized. The K(i) value of Pro-TBODA, Ala-TBODA, and Sar-TBODA was 0.5, microM, 1.6 microM, and 12mM, respectively. The crystal structure of, enzyme-Pro-TBODA complex was determined. Pro-TBODA was located at the, active site. Four electrostatic interactions were located between the, enzyme and the amino group of Pro inhibitors (Glu204:0E1-N:Inh, Glu204:0E2-N:Inh, Glu232:0E1-N:Inh, and Gly46:O-N:Inh), and the residue of, the inhibitors was inserted into the hydrophobic pocket composed of, Phe139, Leu141, Leu146, Tyr149, Tyr150, and Phe236. The roles of Phe139, Tyr149, and Phe236 in the hydrophobic pocket and Glu204 and Glu232 in the, electrostatic interactions were confirmed by site-directed mutagenesis, which indicated that the molecular recognition of proline is achieved, through four electrostatic interactions and an insertion in the, hydrophobic pocket of the enzyme.
<StructureSection load='1wm1' size='340' side='right'caption='[[1wm1]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1wm1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WM1 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PTB:(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)[(2R)-PYRROLIDIN-2-YL]METHANONE'>PTB</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wm1 OCA], [https://pdbe.org/1wm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wm1 RCSB], [https://www.ebi.ac.uk/pdbsum/1wm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wm1 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PIP_SERMA PIP_SERMA] Specifically catalyzes the removal of N-terminal proline residues from peptides.
== 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/wm/1wm1_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=1wm1 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1WM1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with PTB as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Prolyl_aminopeptidase Prolyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.5 3.4.11.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WM1 OCA].
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor., Inoue T, Ito K, Tozaka T, Hatakeyama S, Tanaka N, Nakamura KT, Yoshimoto T, Arch Biochem Biophys. 2003 Aug 15;416(2):147-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12893291 12893291]
[[Category: Large Structures]]
[[Category: Prolyl aminopeptidase]]
[[Category: Serratia marcescens]]
[[Category: Serratia marcescens]]
[[Category: Single protein]]
[[Category: Hatakeyama S]]
[[Category: Hatakeyama, S.]]
[[Category: Inoue T]]
[[Category: Inoue, T.]]
[[Category: Ito K]]
[[Category: Ito, K.]]
[[Category: Nakajima Y]]
[[Category: Nakajima, Y.]]
[[Category: Nakamura KT]]
[[Category: Nakamura, K.T.]]
[[Category: Tanaka N]]
[[Category: Tanaka, N.]]
[[Category: Tozaka T]]
[[Category: Tozaka, T.]]
[[Category: Yoshimoto T]]
[[Category: Yoshimoto, T.]]
[[Category: PTB]]
[[Category: complex with inhibitor]]
[[Category: proline iminopeptidase]]
 
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