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 

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This is version 1.3 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: https://doi.org/10.1126/science.1063601
  • Primary Citation of Related Structures:  
    1JCJ, 1JCL

  • 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYRIBOSE-PHOSPHATE ALDOLASE
A, B
260Escherichia coliMutation(s): 1 
EC: 4.1.2.4
UniProt
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Explore P0A6L0 
Go to UniProtKB:  P0A6L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6L0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
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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Ligand Structure Quality Assessment 


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
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations