M. jannaschii ADH synthase complexed with F1,6P

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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Structure of 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid synthase, a catalyst in the archaeal pathway for the biosynthesis of aromatic amino acids.

Morar, M.White, R.H.Ealick, S.E.

(2007) Biochemistry 46: 10562-10571

  • DOI: https://doi.org/10.1021/bi700934v
  • Primary Citation of Related Structures:  
    2QJG, 2QJH, 2QJI

  • PubMed Abstract: 

    Genes responsible for the generation of 3-dehydroquinate (DHQ), an early metabolite in the established shikimic pathway of aromatic amino acid biosynthesis, are absent in most euryarchaeotes. Alternative gene products, Mj0400 and Mj1249, have been identified in Methanocaldococcus jannaschii as the enzymes involved in the synthesis of DHQ. 2-Amino-3,7-dideoxy-d-threo-hept-6-ulosonic acid (ADH) synthase, the product of the Mj0400 gene, catalyzes a transaldol reaction between 6-deoxy-5-ketofructose 1-phosphate and l-aspartate semialdehyde to yield ADH. Dehydroquinate synthase II, the product of the Mj1249 gene, then catalyzes deamination and cyclization of ADH, resulting in DHQ, which is fed into the canonical pathway. Three crystal structures of ADH synthase were determined in this work: a complex with a substrate analogue, fructose 1,6-bisphosphate, a complex with dihydroxyacetone phosphate (DHAP), thought to be a product of fructose 1-phosphate cleavage, and a native structure containing copurified ligands, modeled as DHAP and glycerol. On the basis of the structural analysis and comparison of the enzyme with related aldolases, ADH synthase is classified as a new member of the class I aldolase superfamily. The description of the active site allows for the identification and characterization of possible catalytic residues, Lys184, which is responsible for formation of the Schiff base intermediate, and Asp33 and Tyr153, which are candidates for the general acid/base catalysis.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative aldolase MJ0400273Methanocaldococcus jannaschiiMutation(s): 0 
EC: 4.2.1 (PDB Primary Data), (UniProt)
Find proteins for Q57843 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57843 
Go to UniProtKB:  Q57843
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57843
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on F2P

Download Ideal Coordinates CCD File 
AA [auth L]
BA [auth M]
CA [auth N]
DA [auth O]
EA [auth F]
AA [auth L],
BA [auth M],
CA [auth N],
DA [auth O],
EA [auth F],
FA [auth G],
GA [auth H],
HA [auth I],
IA [auth J],
JA [auth P],
KA [auth Q],
LA [auth R],
MA [auth S],
NA [auth T],
U [auth A],
V [auth B],
W [auth C],
X [auth D],
Y [auth E],
Z [auth K]
C6 H16 O12 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.45α = 89.4
b = 102.77β = 85.83
c = 156.41γ = 82.05
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance