1JCJ

OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.168 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Observation of covalent intermediates in an enzyme mechanism at atomic resolution.

Heine, A.DeSantis, G.Luz, J.G.Mitchell, M.Wong, C.H.Wilson, I.A.

(2001) Science 294: 369-374

  • DOI: 10.1126/science.1063601
  • Primary Citation of Related Structures:  
    1JCL, 1JCJ

  • 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 ...

    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.


    Organizational Affiliation

    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEOXYRIBOSE-PHOSPHATE ALDOLASEA, B260Escherichia coliMutation(s): 1 
EC: 4.1.2.4
UniProt
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Explore P0A6L0 
Go to UniProtKB:  P0A6L0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HPD
Query on HPD

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE
C5 H13 O7 P
YCHBTVQJICBXEI-CRCLSJGQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.168 
  • R-Value Observed: 0.142 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.54α = 90
b = 41.99β = 98.32
c = 144.87γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance