1JCJ

OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.168 

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

  • 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 intermed ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYRIBOSE-PHOSPHATE ALDOLASE
A, B
260Escherichia coli (strain K12)Gene Names: deoC (dra, thyR)
EC: 4.1.2.4
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6L0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HPD
Query on HPD

Download SDF File 
Download CCD File 
A, B
1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE
OPEN FORM OF 2'-DEOXY-RIBOFURANOSE-5'-PHOSPHATE
C5 H13 O7 P
YCHBTVQJICBXEI-CRCLSJGQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.540α = 90.00
b = 41.990β = 98.32
c = 144.870γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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