3fvz: Difference between revisions
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The | ==Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL)== | ||
<StructureSection load='3fvz' size='340' side='right'caption='[[3fvz]], [[Resolution|resolution]] 2.35Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3fvz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FVZ FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fw0|3fw0]], [[1phm|1phm]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pam ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidylamidoglycolate_lyase Peptidylamidoglycolate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.5 4.3.2.5] </span></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=3fvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fvz OCA], [https://pdbe.org/3fvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fvz RCSB], [https://www.ebi.ac.uk/pdbsum/3fvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fvz ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/AMD_RAT AMD_RAT]] Bifunctional enzyme that catalyzes 2 sequential steps in C-terminal alpha-amidation of peptides. The monooxygenase part produces an unstable peptidyl(2-hydroxyglycine) intermediate that is dismutated to glyoxylate and the corresponding desglycine peptide amide by the lyase part. C-terminal amidation of peptides such as neuropeptides is essential for full biological activity. | |||
== 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/fv/3fvz_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=3fvz ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Many neuropeptides and peptide hormones require amidation of their carboxy terminal for full biological activity. The enzyme peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL; EC 4.3.2.5) catalyzes the second and last step of this reaction, N-dealkylation of the peptidyl-alpha-hydroxyglycine to generate the alpha-amidated peptide and glyoxylate. Here we report the X-ray crystal structure of the PAL catalytic core (PALcc) alone and in complex with the nonpeptidic substrate alpha-hydroxyhippuric acid. The structures show that PAL folds as a six-bladed beta-propeller. The active site is formed by a Zn(II) ion coordinated by three histidine residues; the substrate binds to this site with its alpha-hydroxyl group coordinated to the Zn(II) ion. The structures also reveal a tyrosine residue (Tyr(654)) at the active site as the catalytic base for hydroxyl deprotonation, an unusual role for tyrosine. A reaction mechanism is proposed based on this structural data and validated by biochemical analysis of site-directed PALcc mutants. | |||
Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.,Chufan EE, De M, Eipper BA, Mains RE, Amzel LM Structure. 2009 Jul 15;17(7):965-73. PMID:19604476<ref>PMID:19604476</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3fvz" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Monooxygenase 3D structures|Monooxygenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Buffalo rat]] | |||
[[Category: Large Structures]] | |||
[[Category: Peptidylamidoglycolate lyase]] | |||
[[Category: Amzel, L M]] | |||
[[Category: Chufan, E E]] | |||
[[Category: De, M]] | |||
[[Category: Eipper, B A]] | |||
[[Category: Mains, R E]] | |||
[[Category: Beta propeller]] | |||
[[Category: Cleavage on pair of basic residue]] | |||
[[Category: Cytoplasmic vesicle]] | |||
[[Category: Glycoprotein]] | |||
[[Category: Hg-mad]] | |||
[[Category: Lyase]] | |||
[[Category: Membrane]] | |||
[[Category: Metal-binding]] | |||
[[Category: Monooxygenase]] | |||
[[Category: Multifunctional enzyme]] | |||
[[Category: Oxidoreductase]] | |||
[[Category: Peptide amidation]] | |||
[[Category: Phosphoprotein]] | |||
[[Category: Sulfation]] | |||
[[Category: Transmembrane]] | |||
[[Category: Vitamin c]] | |||
[[Category: Zn-mad]] | |||
