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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
5541
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pubmed:dateCreated |
2001-10-12
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pubmed:databankReference |
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pubmed:abstractText |
In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.
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pubmed:grant |
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pubmed:commentsCorrections |
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Oct
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pubmed:issn |
0036-8075
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:day |
12
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pubmed:volume |
294
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
369-74
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pubmed:dateRevised |
2008-11-21
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pubmed:meshHeading |
pubmed-meshheading:11598300-Aldehyde-Lyases,
pubmed-meshheading:11598300-Amino Acid Substitution,
pubmed-meshheading:11598300-Binding Sites,
pubmed-meshheading:11598300-Catalysis,
pubmed-meshheading:11598300-Chemistry, Physical,
pubmed-meshheading:11598300-Crystallization,
pubmed-meshheading:11598300-Crystallography, X-Ray,
pubmed-meshheading:11598300-Escherichia coli,
pubmed-meshheading:11598300-Hydrogen Bonding,
pubmed-meshheading:11598300-Hydrogen-Ion Concentration,
pubmed-meshheading:11598300-Ligands,
pubmed-meshheading:11598300-Lysine,
pubmed-meshheading:11598300-Models, Chemical,
pubmed-meshheading:11598300-Mutagenesis, Site-Directed,
pubmed-meshheading:11598300-Mutation,
pubmed-meshheading:11598300-Nuclear Magnetic Resonance, Biomolecular,
pubmed-meshheading:11598300-Physicochemical Phenomena,
pubmed-meshheading:11598300-Protein Conformation,
pubmed-meshheading:11598300-Protein Folding,
pubmed-meshheading:11598300-Protein Structure, Tertiary,
pubmed-meshheading:11598300-Protons,
pubmed-meshheading:11598300-Ribosemonophosphates,
pubmed-meshheading:11598300-Schiff Bases,
pubmed-meshheading:11598300-Water
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pubmed:year |
2001
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pubmed:articleTitle |
Observation of covalent intermediates in an enzyme mechanism at atomic resolution.
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pubmed:affiliation |
Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.,
Research Support, Non-U.S. Gov't
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