1m0p

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[[Image:1m0p.gif|left|200px]]
 
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==Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-phenylethanephosphonate==
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The line below this paragraph, containing "STRUCTURE_1m0p", creates the "Structure Box" on the page.
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<StructureSection load='1m0p' size='340' side='right'caption='[[1m0p]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1m0p]] 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=1M0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M0P FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.6&#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=ELP:(1R)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]-1-PHENYLETHYLPHOSPHONIC+ACID'>ELP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_1m0p| PDB=1m0p | SCENE= }}
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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=1m0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0p OCA], [https://pdbe.org/1m0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m0p RCSB], [https://www.ebi.ac.uk/pdbsum/1m0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0p ProSAT]</span></td></tr>
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</table>
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'''Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-phenylethanephosphonate'''
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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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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m0/1m0p_consurf.spt"</scriptWhenChecked>
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1M0P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0P OCA].
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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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==Reference==
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</jmolCheckbox>
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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://www.ncbi.nlm.nih.gov/pubmed/12369820 12369820]
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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=1m0p 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: 3d-structure]]
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[[Category: Decarboxylase]]
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[[Category: Pyridoxal phosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 00:29:33 2008''
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Current revision

Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-phenylethanephosphonate

PDB ID 1m0p

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