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| | <StructureSection load='1x7d' size='340' side='right'caption='[[1x7d]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='1x7d' size='340' side='right'caption='[[1x7d]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1x7d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X7D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1X7D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1x7d]] 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=1X7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X7D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <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>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u7h|1u7h]]</div></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=1x7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x7d OCA], [https://pdbe.org/1x7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x7d RCSB], [https://www.ebi.ac.uk/pdbsum/1x7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x7d ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ORNITHINE CYCLASE (DEAMINATING) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_cyclodeaminase Ornithine cyclodeaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.12 4.3.1.12] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1x7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x7d OCA], [http://pdbe.org/1x7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x7d RCSB], [http://www.ebi.ac.uk/pdbsum/1x7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1x7d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens putidus flugge 1886]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ornithine cyclodeaminase]] | + | [[Category: Pseudomonas putida]] |
| - | [[Category: Alam, S]] | + | [[Category: Alam S]] |
| - | [[Category: Frey, P A]] | + | [[Category: Frey PA]] |
| - | [[Category: Goodman, J L]] | + | [[Category: Goodman JL]] |
| - | [[Category: Ruzicka, F J]] | + | [[Category: Ruzicka FJ]] |
| - | [[Category: Wang, S]] | + | [[Category: Wang S]] |
| - | [[Category: Wedekind, J E]] | + | [[Category: Wedekind JE]] |
| - | [[Category: Helix bundle]]
| + | |
| - | [[Category: Beta barrel]]
| + | |
| - | [[Category: Binds l-ornithine]]
| + | |
| - | [[Category: Binds l-proline]]
| + | |
| - | [[Category: Binds nad+]]
| + | |
| - | [[Category: Deaminase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
1x7d is a 2 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.6Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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:15518536[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Jensen JV, Wendisch VF. Ornithine cyclodeaminase-based proline production by Corynebacterium glutamicum. Microb Cell Fact. 2013 Jun 28;12:63. PMID:23806148 doi:10.1186/1475-2859-12-63
- ↑ Goodman JL, Wang S, Alam S, Ruzicka FJ, Frey PA, Wedekind JE. Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family. Biochemistry. 2004 Nov 9;43(44):13883-91. PMID:15518536 doi:10.1021/bi048207i
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