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New page: left|200px<br /><applet load="1ynu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ynu, resolution 2.25Å" /> '''Crystal structure of...
 
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[[Image:1ynu.gif|left|200px]]<br /><applet load="1ynu" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ynu, resolution 2.25&Aring;" />
'''Crystal structure of apple ACC synthase in complex with L-vinylglycine'''<br />


==Overview==
==Crystal structure of apple ACC synthase in complex with L-vinylglycine==
L-Vinylglycine (L-VG) is both a substrate for and a mechanism-based, inhibitor of 1-aminocyclopropane-1-carboxylate (ACC) synthase. The ratio, of the rate constants for catalytic conversion to alpha-ketobutyrate and, ammonia to inactivation is 500/1. The crystal structure of the covalent, adduct of the inactivated enzyme was determined at 2.25 Angstroms, resolution. The active site contains an external aldimine of the adduct of, L-VG with the pyridoxal 5'-phosphate cofactor. The side chain gamma-carbon, of L-VG is covalently bound to the epsilon-amino group of Lys273. This, species corresponds to one of the two alternatives proposed by Feng and, Kirsch [Feng, L. and Kirsch, J.F. (2000) L-Vinylglycine is an alternative, substrate as well as a mechanism-based inhibitor of, 1-aminocyclopropane-1-carboxylate synthase. Biochemistry 39, 2436-2444], and presumably results from Michael addition to a vinylglycine ketimine, intermediate.
<StructureSection load='1ynu' size='340' side='right'caption='[[1ynu]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ynu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Malus_domestica Malus domestica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNU 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]] 2.25&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PY4:2-[O-PHOSPHONOPYRIDOXYL]-AMINO-+BUTYRIC+ACID'>PY4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1ynu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynu OCA], [https://pdbe.org/1ynu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynu RCSB], [https://www.ebi.ac.uk/pdbsum/1ynu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynu ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/1A1C_MALDO 1A1C_MALDO] Catalyzes the formation of 1-aminocyclopropane-1-carboxylate, a direct precursor of ethylene in higher plants.
== 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/yn/1ynu_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ynu ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
L-Vinylglycine (L-VG) is both a substrate for and a mechanism-based inhibitor of 1-aminocyclopropane-1-carboxylate (ACC) synthase. The ratio of the rate constants for catalytic conversion to alpha-ketobutyrate and ammonia to inactivation is 500/1. The crystal structure of the covalent adduct of the inactivated enzyme was determined at 2.25 Angstroms resolution. The active site contains an external aldimine of the adduct of L-VG with the pyridoxal 5'-phosphate cofactor. The side chain gamma-carbon of L-VG is covalently bound to the epsilon-amino group of Lys273. This species corresponds to one of the two alternatives proposed by Feng and Kirsch [Feng, L. and Kirsch, J.F. (2000) L-Vinylglycine is an alternative substrate as well as a mechanism-based inhibitor of 1-aminocyclopropane-1-carboxylate synthase. Biochemistry 39, 2436-2444] and presumably results from Michael addition to a vinylglycine ketimine intermediate.


==About this Structure==
Structure of ACC synthase inactivated by the mechanism-based inhibitor L-vinylglycine.,Capitani G, Tschopp M, Eliot AC, Kirsch JF, Grutter MG FEBS Lett. 2005 Apr 25;579(11):2458-62. PMID:15848188<ref>PMID:15848188</ref>
1YNU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Malus_x_domestica Malus x domestica] with NI, K, PY4 and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-aminocyclopropane-1-carboxylate_synthase 1-aminocyclopropane-1-carboxylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.14 4.4.1.14] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YNU OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure of ACC synthase inactivated by the mechanism-based inhibitor L-vinylglycine., Capitani G, Tschopp M, Eliot AC, Kirsch JF, Grutter MG, FEBS Lett. 2005 Apr 25;579(11):2458-62. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15848188 15848188]
</div>
[[Category: 1-aminocyclopropane-1-carboxylate synthase]]
<div class="pdbe-citations 1ynu" style="background-color:#fffaf0;"></div>
[[Category: Malus x domestica]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Capitani, G.]]
__TOC__
[[Category: Eliot, A.C.]]
</StructureSection>
[[Category: Grutter, M.G.]]
[[Category: Large Structures]]
[[Category: Kirsch, J.F.]]
[[Category: Malus domestica]]
[[Category: Tschopp, M.]]
[[Category: Capitani G]]
[[Category: K]]
[[Category: Eliot AC]]
[[Category: NI]]
[[Category: Grutter MG]]
[[Category: PY4]]
[[Category: Kirsch JF]]
[[Category: TRS]]
[[Category: Tschopp M]]
[[Category: lyase]]
 
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Latest revision as of 07:44, 23 October 2024

Crystal structure of apple ACC synthase in complex with L-vinylglycine

1ynu, resolution 2.25Å

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