3ah3

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[[Image:3ah3.png|left|200px]]
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==Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution==
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<StructureSection load='3ah3' size='340' side='right' caption='[[3ah3]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3ah3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AH3 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x0l|1x0l]]</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LR5-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Homoisocitrate_dehydrogenase Homoisocitrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.87 1.1.1.87] </span></td></tr>
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<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=3ah3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ah3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ah3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ah3 PDBsum]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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HICDH (homoisocitrate dehydrogenase), which is involved in lysine biosynthesis through alpha-aminoadipate, is a paralogue of IPMDH [3-IPM (3-isopropylmalate) dehydrogenase], which is involved in leucine biosynthesis. TtHICDH (Thermus thermophilus HICDH) can recognize isocitrate, as well as homoisocitrate, as the substrate, and also shows IPMDH activity, although at a considerably decreased rate. In the present study, the promiscuous TtHICDH was evolved into an enzyme showing distinct IPMDH activity by directed evolution using a DNA-shuffling technique. Through five repeats of DNA shuffling/screening, variants that allowed Escherichia coli C600 (leuB) to grow on a minimal medium in 2 days were obtained. One of the variants LR5-1, with eight amino acid replacements, was found to possess a 65-fold increased k(cat)/K(m) value for 3-IPM, compared with TtHICDH. Introduction of a single back-replacement H15Y change caused a further increase in the k(cat)/K(m) value and a partial recovery of the decreased thermotolerance of LR5-1. Site-directed mutagenesis revealed that most of the amino acid replacements found in LR5-1 effectively increased IPMDH activity; replacements around the substrate-binding site contributed to the improved recognition for 3-IPM, and other replacements at sites away from the substrate-binding site enhanced the turnover number for the IPMDH reaction. The crystal structure of LR5-1 was determined at 2.4 A resolution and revealed that helix alpha4 was displaced in a manner suitable for recognition of the hydrophobic gamma-moiety of 3-IPM. On the basis of the crystal structure, possible reasons for enhancement of the turnover number are discussed.
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{{STRUCTURE_3ah3| PDB=3ah3 | SCENE= }}
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Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution.,Suzuki Y, Asada K, Miyazaki J, Tomita T, Kuzuyama T, Nishiyama M Biochem J. 2010 Oct 11;431(3):401-10. PMID:20735360<ref>PMID:20735360</ref>
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===Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution===
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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>
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{{ABSTRACT_PUBMED_20735360}}
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==About this Structure==
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[[3ah3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AH3 OCA].
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==See Also==
==See Also==
*[[Isocitrate dehydrogenase|Isocitrate dehydrogenase]]
*[[Isocitrate dehydrogenase|Isocitrate dehydrogenase]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:020735360</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Homoisocitrate dehydrogenase]]
[[Category: Homoisocitrate dehydrogenase]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]

Revision as of 09:21, 5 November 2014

Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution

3ah3, resolution 2.40Å

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