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1m0n

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(New page: 200px<br /><applet load="1m0n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m0n, resolution 2.2&Aring;" /> '''Structure of Dialkylg...)
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[[Image:1m0n.jpg|left|200px]]<br /><applet load="1m0n" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1m0n, resolution 2.2&Aring;" />
 
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'''Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate'''<br />
 
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==Overview==
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==Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate==
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The kinetics of inhibition of dialkylglycine decarboxylase by five, aminophosphonate inhibitors are presented. Two of these, [(R)-1-amino-1-methylpropanephosphonate and (S)-1-aminoethanephosphonate], are slow binding inhibitors. The inhibitors follow a mechanism in which a, weak complex is rapidly formed, followed by slow isomerization to the, tight complex. Here, the tight complexes are bound 10-fold more tightly, than the weak, initial complexes. The slow onset inhibition occurs with, t(1/2) values of 1.3 and 0.55 min at saturating inhibitor concentrations, for the AMPP and S-AEP inhibitors, respectively, while dissociation of, these inhibitor complexes occurs with t(1/2) values of 13 and 4.6 min, respectively. The X-ray structures of four of the inhibitors in complex, with dialkylglycine decarboxylase have been determined to resolutions, ranging from 2.6 to 2.0 A, and refined to R-factors of 14.5-19.5%. These, structures show variation in the active site structure with inhibitor side, chain size and slow binding character. It is proposed that the slow, binding behavior originates in an isomerization from an initial complex in, which the PLP pyridine nitrogen-D243 OD2 distance is approximately 2.9 A, to one in which it is approximately 2.7 A. The angles that the C-P bonds, make with the p orbitals of the aldimine pi system are correlated with the, reactivities of the analogous amino acid substrates, suggesting a role for, stereoelectronic effects in Schiff base reactivity.
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<StructureSection load='1m0n' size='340' side='right'caption='[[1m0n]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1m0n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M0N FirstGlance]. <br>
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1M0N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia] with K, NA and HCP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M0N 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]] 2.2&#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=HCP:1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]CYCLOPENTYLPHOSPHONIC+ACID'>HCP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1m0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0n OCA], [https://pdbe.org/1m0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m0n RCSB], [https://www.ebi.ac.uk/pdbsum/1m0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0n ProSAT]</span></td></tr>
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Aminophosphonate inhibitors of dialkylglycine decarboxylase: structural basis for slow binding inhibition., Liu W, Rogers CJ, Fisher AJ, Toney MD, Biochemistry. 2002 Oct 15;41(41):12320-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12369820 12369820]
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</table>
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[[Category: 2,2-dialkylglycine decarboxylase (pyruvate)]]
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== Function ==
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[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.
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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/m0/1m0n_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=1m0n ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Burkholderia cepacia]]
[[Category: Burkholderia cepacia]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Fisher, A.J.]]
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[[Category: Fisher AJ]]
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[[Category: Liu, W.]]
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[[Category: Liu W]]
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[[Category: Rogers, C.J.]]
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[[Category: Rogers CJ]]
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[[Category: Toney, M.D.]]
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[[Category: Toney MD]]
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[[Category: HCP]]
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[[Category: K]]
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[[Category: NA]]
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[[Category: 3d-structure]]
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[[Category: decarboxylase]]
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[[Category: pyridoxal phosphate]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:02:31 2007''
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Current revision

Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate

PDB ID 1m0n

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