1njj

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{{STRUCTURE_1njj| PDB=1njj | SCENE= }}
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==Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418==
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===Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418===
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<StructureSection load='1njj' size='340' side='right' caption='[[1njj]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
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{{ABSTRACT_PUBMED_12672797}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1njj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_gambiense Trypanosoma brucei gambiense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJJ FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GET:GENETICIN'>GET</scene>, <scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qu4|1qu4]], [[1f3t|1f3t]]</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1njj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njj RCSB], [http://www.ebi.ac.uk/pdbsum/1njj PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1njj_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Ornithine decarboxylase (ODC) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure of Trypanosoma brucei ODC in complex with d-ornithine (d-Orn), a substrate analog, and G418 (Geneticin), a weak non-competitive inhibitor, was determined to 2.5-A resolution. d-Orn forms a Schiff base with PLP, and the side chain is in a similar position to that observed for putrescine and alpha-difluoromethylornithine in previous T. brucei ODC structures. The d-Orn carboxylate is positioned on the solvent-exposed side of the active site (si face of PLP), and Gly-199, Gly-362, and His-197 are the only residues within 4.2 A of this moiety. This structure confirms predictions that the carboxylate of d-Orn binds on the si face of PLP, and it supports a model in which the carboxyl group of the substrate l-Orn would be buried on the re face of the cofactor in a pocket that includes Phe-397, Tyr-389, Lys-69 (methylene carbons), and Asp-361. Electron density for G418 was observed at the boundary between the two domains within each ODC monomer. A ten-amino acid loop region (392-401) near the 2-fold axis of the dimer interface, which contributes several residues that form the active site, is disordered in this structure. The disordering of residues in the active site provides a potential mechanism for inhibition by G418 and suggests that allosteric inhibition from this site is feasible.
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==About this Structure==
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X-ray structure determination of Trypanosoma brucei ornithine decarboxylase bound to D-ornithine and to G418: insights into substrate binding and ODC conformational flexibility.,Jackson LK, Goldsmith EJ, Phillips MA J Biol Chem. 2003 Jun 13;278(24):22037-43. Epub 2003 Apr 2. PMID:12672797<ref>PMID:12672797</ref>
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[[1njj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_gambiense Trypanosoma brucei gambiense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJJ OCA].
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
==See Also==
==See Also==
*[[Ornithine decarboxylase|Ornithine decarboxylase]]
*[[Ornithine decarboxylase|Ornithine decarboxylase]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:012672797</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Ornithine decarboxylase]]
[[Category: Ornithine decarboxylase]]
[[Category: Trypanosoma brucei gambiense]]
[[Category: Trypanosoma brucei gambiense]]

Revision as of 15:22, 29 September 2014

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

1njj, resolution 2.45Å

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