1JCL

OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION

Summary for 1JCL

• Entry DOI: 10.2210/pdb1jcl/pdb
• Related: 1JCJ
• Descriptor: DEOXYRIBOSE-PHOSPHATE ALDOLASE, 1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE (3 entities in total)
• Functional Keywords: alpha-beta tim barrel, lyase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A6L0
• Total number of polymer chains: 2
• Total formula weight: 56246.18

Authors

Heine, A.,DeSantis, G.,Luz, J.G.,Mitchell, M.,Wong, C.-H.,Wilson, I.A. (deposition date: 2001-06-09, release date: 2001-10-31, Last modification date: 2024-11-20)

Primary citation

Heine, A.,DeSantis, G.,Luz, J.G.,Mitchell, M.,Wong, C.H.,Wilson, I.A.
Observation of covalent intermediates in an enzyme mechanism at atomic resolution.
Science, 294:369-374, 2001

PubMed Abstract: 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.

PubMed: 11598300
DOI: 10.1126/science.1063601

Experimental method

X-RAY DIFFRACTION (1.05 Å)