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1u7h

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[[Image:1u7h.jpg|left|200px]]
 
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==Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida==
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The line below this paragraph, containing "STRUCTURE_1u7h", creates the "Structure Box" on the page.
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<StructureSection load='1u7h' size='340' side='right'caption='[[1u7h]], [[Resolution|resolution]] 1.80&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'>[[1u7h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U7H 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]] 1.8&#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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
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{{STRUCTURE_1u7h| PDB=1u7h | 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=1u7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u7h OCA], [https://pdbe.org/1u7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u7h RCSB], [https://www.ebi.ac.uk/pdbsum/1u7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u7h ProSAT]</span></td></tr>
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</table>
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'''Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida'''
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== Function ==
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[https://www.uniprot.org/uniprot/OCD_PSEPK OCD_PSEPK] Catalyzes the conversion of L-ornithine into L-proline with release of ammonia. Is likely involved in the L-ornithine degradation pathway that allows P.putida to utilize this compound as sole carbon and nitrogen source.<ref>PMID:23806148</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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Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-dimensional fold has not been reported. Here we describe the crystal structure of ornithine cyclodeaminase in complex with NADH, refined to 1.80 A resolution. The enzyme consists of a homodimeric fold whose subunits comprise two functional regions: (i) a novel substrate-binding domain whose antiparallel beta-strands form a 14-stranded barrel at the oligomeric interface and (ii) a canonical Rossmann fold that interacts with a single dinucleotide positioned for re hydride transfer. The adenosyl moiety of the cofactor resides in a solvent-exposed crevice on the protein surface and makes contact with a "domain-swapped"-like coil-helix module originating from the dyad-related molecule. Diffraction data were also collected to 1.60 A resolution on crystals grown in the presence of l-ornithine. The structure revealed that the substrate carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112. In addition, the ammonia leaving group hydrogen bonds to the side chain of Asp228 and the site of hydride transfer is 3.8 A from C4 of the nicotinamide. The absence of an appropriately positioned water suggested that a previously proposed mechanism that calls for hydrolytic elimination of the imino intermediate must be reconsidered. A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins.
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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/u7/1u7h_consurf.spt"</scriptWhenChecked>
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1U7H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U7H 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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Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family., Goodman JL, Wang S, Alam S, Ruzicka FJ, Frey PA, Wedekind JE, Biochemistry. 2004 Nov 9;43(44):13883-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15518536 15518536]
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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=1u7h ConSurf].
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[[Category: Ornithine cyclodeaminase]]
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
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[[Category: Single protein]]
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[[Category: Alam S]]
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[[Category: Alam, S.]]
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[[Category: Frey PA]]
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[[Category: Frey, P A.]]
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[[Category: Goodman JL]]
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[[Category: Goodman, J L.]]
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[[Category: Ruzicka FJ]]
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[[Category: Ruzicka, F J.]]
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[[Category: Wang S]]
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[[Category: Wang, S.]]
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[[Category: Wedekind JE]]
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[[Category: Wedekind, J E.]]
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[[Category: Beta barrel]]
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[[Category: Binds l-ornithine]]
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[[Category: Binds l-pro]]
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[[Category: Binds nad+]]
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[[Category: Deaminase]]
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[[Category: Helix bundle]]
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[[Category: Rossmann fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 10:51:06 2008''
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Current revision

Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida

PDB ID 1u7h

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