5HWM

Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.097 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 4UR8 - determined by Taberman, H., Parkkinen, T., Hakulinen, N., Rouvinen, J.  

Literature

Structure and function of a decarboxylating Agrobacterium tumefaciens keto-deoxy-d-galactarate dehydratase.

Taberman, H.Andberg, M.Parkkinen, T.Janis, J.Penttila, M.Hakulinen, N.Koivula, A.Rouvinen, J.

(2014) Biochemistry 53: 8052-8060

  • DOI: 10.1021/bi501290k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both d-glucuronic and d-galacturonic acid. The corresponding gene coding for At keto-deoxy-d-galactarate (KDG) dehydratase is located in the same gene ...

    Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both d-glucuronic and d-galacturonic acid. The corresponding gene coding for At keto-deoxy-d-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 Å, 1.5 Å, and 2.1 Å resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.


    Organizational Affiliation

    Department of Chemistry, University of Eastern Finland , FI-80101 Joensuu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable 5-dehydro-4-deoxyglucarate dehydratase
A, B, C, D
311Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
EC: 4.2.1.41
Find proteins for Q8UB77 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q8UB77
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OOG
Query on OOG

Download SDF File 
Download CCD File 
A, B, C, D
2-OXOADIPIC ACID
C6 H8 O5
FGSBNBBHOZHUBO-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
C, D
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.097 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 169.520α = 90.00
b = 119.030β = 112.24
c = 74.280γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release