1u7h: Difference between revisions
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<StructureSection load='1u7h' size='340' side='right' caption='[[1u7h]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='1u7h' size='340' side='right' caption='[[1u7h]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1u7h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[1u7h]] 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=1U7H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U7H FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></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='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='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 | <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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u7h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u7h RCSB], [http://www.ebi.ac.uk/pdbsum/1u7h PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u7h OCA], [http://pdbe.org/1u7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u7h RCSB], [http://www.ebi.ac.uk/pdbsum/1u7h PDBsum]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1u7h" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus fluorescens putidus flugge 1886]] | |||
[[Category: Ornithine cyclodeaminase]] | [[Category: Ornithine cyclodeaminase]] | ||
[[Category: Alam, S]] | [[Category: Alam, S]] | ||
[[Category: Frey, P A]] | [[Category: Frey, P A]] | ||
Revision as of 14:18, 11 September 2015
Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putidaStructure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida
Structural highlights
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 PubMedOrnithine 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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