3b8i

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[[Image:3b8i.jpg|left|200px]]
 
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==Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.==
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The line below this paragraph, containing "STRUCTURE_3b8i", creates the "Structure Box" on the page.
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<StructureSection load='3b8i' size='340' side='right'caption='[[3b8i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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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'>[[3b8i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B8I FirstGlance]. <br>
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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]] 1.9&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>
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{{STRUCTURE_3b8i| PDB=3b8i | 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=3b8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8i OCA], [https://pdbe.org/3b8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b8i RCSB], [https://www.ebi.ac.uk/pdbsum/3b8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8i ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.'''
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== Function ==
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[https://www.uniprot.org/uniprot/OADC_PSEAE OADC_PSEAE] Catalyzes the decarboxylation of oxaloacetate into pyruvate with high efficiency. Is also able to decarboxylate 3-methyloxaloacetate. Seems to play a role in maintaining cellular concentrations of bicarbonate and pyruvate.<ref>PMID:18081320</ref>
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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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Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member of the PEP mutase/isocitrate lyase superfamily and therefore targeted for investigation. Substrate screens ruled out overlap with known catalytic functions of superfamily members. The crystal structure of PA4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and Mg2+ was determined at 1.9 A resolution. As with other PEP mutase/isocitrate lyase superfamily members, the protein assembles into a dimer of dimers with each subunit adopting an alpha/beta barrel fold and two subunits swapping their barrel's C-terminal alpha-helices. Mg2+ and oxalate bind in the same manner as observed with other superfamily members. The active site gating loop, known to play a catalytic role in the PEP mutase and lyase branches of the superfamily, adopts an open conformation. The Nepsilon of His235, an invariant residue in the PA4872 sequence family, is oriented toward a C(2) oxygen of oxalate analogous to the C(3) of a pyruvyl moiety. Deuterium exchange into alpha-oxocarboxylate-containing compounds was confirmed by 1H NMR spectroscopy. Having ruled out known activities, the involvement of a pyruvate enolate intermediate suggested a decarboxylase activity of an alpha-oxocarboxylate substrate. Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM). Genome context of the fourteen sequence family members indicates that the enzyme is used by select group of Gram-negative bacteria to maintain cellular concentrations of bicarbonate and pyruvate; however the decarboxylation activity cannot be attributed to a pathway common to the various bacterial species.
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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/b8/3b8i_consurf.spt"</scriptWhenChecked>
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3B8I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8I 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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Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily., Narayanan BC, Niu W, Han Y, Zou J, Mariano PS, Dunaway-Mariano D, Herzberg O, Biochemistry. 2008 Jan 8;47(1):167-82. Epub 2007 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18081320 18081320]
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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=3b8i ConSurf].
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[[Category: Oxaloacetate decarboxylase]]
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<div style="clear:both"></div>
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[[Category: Pseudomonas aeruginosa]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Herzberg, O]]
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__TOC__
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[[Category: Narayanan, B C.]]
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</StructureSection>
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[[Category: Alpha/beta barrel]]
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[[Category: Large Structures]]
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[[Category: Helix swapping]]
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[[Category: Pseudomonas aeruginosa PAO1]]
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[[Category: Lyase]]
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[[Category: Herzberg O]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 16 23:09:23 2008''
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[[Category: Narayanan BC]]

Current revision

Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.

PDB ID 3b8i

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