4UR8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5HWM


Literature

Structure and Function of a Decarboxylating Agrobacterium Tumefaciens Keto-Deoxy-D-Galactarate Dehydratase.

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

(2014) Biochemistry 53: 8052

  • DOI: https://doi.org/10.1021/bi501290k
  • Primary Citation of Related Structures:  
    4UR7, 4UR8, 5HWJ, 5HWM, 5HWN

  • 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 cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KETO-DEOXY-D-GALACTARATE DEHYDRATASE
A, B, C, D
311Agrobacterium tumefaciensMutation(s): 0 
EC: 4.2.1 (PDB Primary Data), 4.2.1.41 (UniProt)
UniProt
Find proteins for Q8UB77 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q8UB77 
Go to UniProtKB:  Q8UB77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8UB77
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.52α = 90
b = 119.03β = 112.24
c = 74.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2015-01-28
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other