Linked Life Data

11284679

Source:http://linkedlifedata.com/resource/pubmed/id/11284679

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
14
pubmed:dateCreated
2001-4-4
pubmed:databankReference
pubmed:abstractText
Isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate and has negligible activity toward other (R)-malate-type substrates. The S113E mutant of IDH significantly improves its ability to utilize isopropylmalate as a substrate and switches the substrate specificity (k(cat)/K(M)) from isocitrate to isopropylmalate. To understand the structural basis for this switch in substrate specificity, we have determined the crystal structure of IDH S113E in a complex with isopropylmalate, NADP, and Mg(2+) to 2.0 A resolution. On the basis of a comparison with previously determined structures, we identify distinct changes caused by the amino acid substitution and by the binding of substrates. The S113E complex exhibits alterations in global and active site conformations compared with other IDH structures that include loop and helix conformational changes near the active site. In addition, the angle of the hinge that relates the two domains was altered in this structure, which suggests that the S113E substitution and the binding of substrates act together to promote catalysis of isopropylmalate. Ligand binding results in reorientation of the active site helix that contains residues 113 through 116. E113 exhibits new interactions, including van der Waals contacts with the isopropyl group of isopropylmalate and a hydrogen bond with N115, which in turn forms a hydrogen bond with NADP. In addition, the loop and helix regions that bind NADP are altered, as is the loop that connects the NADP binding region to the active site helix, changing the relationship between substrates and enzyme. In combination, these interactions appear to provide the basis for the switch in substrate specificity.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0006-2960
pubmed:author
pubmed:issnType
Print
pubmed:day
10
pubmed:volume
40
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
4234-41
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed-meshheading:11284679-Amino Acid Substitution, pubmed-meshheading:11284679-Binding Sites, pubmed-meshheading:11284679-Catalysis, pubmed-meshheading:11284679-Crystallography, X-Ray, pubmed-meshheading:11284679-Escherichia coli, pubmed-meshheading:11284679-Freezing, pubmed-meshheading:11284679-Glutamic Acid, pubmed-meshheading:11284679-Isocitrate Dehydrogenase, pubmed-meshheading:11284679-Macromolecular Substances, pubmed-meshheading:11284679-Magnesium, pubmed-meshheading:11284679-Malates, pubmed-meshheading:11284679-NADP, pubmed-meshheading:11284679-Protein Structure, Secondary, pubmed-meshheading:11284679-Protein Structure, Tertiary, pubmed-meshheading:11284679-Serine, pubmed-meshheading:11284679-Structure-Activity Relationship, pubmed-meshheading:11284679-Substrate Specificity, pubmed-meshheading:11284679-Tyrosine
pubmed:year
2001
pubmed:articleTitle
Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP.
pubmed:affiliation
Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S.