2QJI

M. jannaschii ADH synthase complexed with dihydroxyacetone phosphate and glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/bi700934v
  • Primary Citation of Related Structures:  

  • 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 id ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative aldolase MJ0400
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
273Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: aroA'
EC: 2.2.1.10
Find proteins for Q57843 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57843
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
13P
Query on 13P

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.244 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 94.144α = 90.05
b = 103.543β = 87.97
c = 153.990γ = 82.04
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance