Linked Life Data

10978154

Source:http://linkedlifedata.com/resource/pubmed/id/10978154

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
35
pubmed:dateCreated
2000-9-28
pubmed:databankReference
pubmed:abstractText
The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0006-2960
pubmed:author
pubmed:issnType
Print
pubmed:day
5
pubmed:volume
39
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
10702-10
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed-meshheading:10978154-Animals, pubmed-meshheading:10978154-Apoenzymes, pubmed-meshheading:10978154-Bacterial Proteins, pubmed-meshheading:10978154-Binding Sites, pubmed-meshheading:10978154-Computer Simulation, pubmed-meshheading:10978154-Crystallography, X-Ray, pubmed-meshheading:10978154-Escherichia coli, pubmed-meshheading:10978154-Glyceraldehyde 3-Phosphate, pubmed-meshheading:10978154-Glyceraldehyde-3-Phosphate Dehydrogenases, pubmed-meshheading:10978154-Holoenzymes, pubmed-meshheading:10978154-Humans, pubmed-meshheading:10978154-Models, Molecular, pubmed-meshheading:10978154-NAD, pubmed-meshheading:10978154-Nephropidae, pubmed-meshheading:10978154-Protein Conformation, pubmed-meshheading:10978154-Structure-Activity Relationship, pubmed-meshheading:10978154-Substrate Specificity
pubmed:year
2000
pubmed:articleTitle
Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes.
pubmed:affiliation
Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale, Memphis, Tennessee 38105, 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., Research Support, Non-U.S. Gov't