3RFV

Crystal structure of Uronate dehydrogenase from Agrobacterium tumefaciens complexed with NADH and product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens.

Parkkinen, T.Boer, H.Janis, J.Andberg, M.Penttila, M.Koivula, A.Rouvinen, J.

(2011) J.Biol.Chem. 286: 27294-27300

  • DOI: 10.1074/jbc.M111.254854
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uronate dehydrogenase from Agrobacterium tumefaciens (AtUdh) belongs to the short-chain dehydrogenase/reductase superfamily and catalyzes the oxidation of D-galacturonic acid and D-glucuronic acid with NAD(+) as a cofactor. We have determined the cry ...

    Uronate dehydrogenase from Agrobacterium tumefaciens (AtUdh) belongs to the short-chain dehydrogenase/reductase superfamily and catalyzes the oxidation of D-galacturonic acid and D-glucuronic acid with NAD(+) as a cofactor. We have determined the crystal structures of an apo-form of AtUdh, a ternary form in complex with NADH and product (substrate-soaked structure), and an inactive Y136A mutant in complex with NAD(+). The crystal structures suggest AtUdh to be a homohexamer, which has also been observed to be the major form in solution. The monomer contains a Rossmann fold, essential for nucleotide binding and a common feature of the short-chain dehydrogenase/reductase family enzymes. The ternary complex structure reveals a product, D-galactaro-1,5-lactone, which is bound above the nicotinamide ring. This product rearranges in solution to D-galactaro-1,4-lactone as verified by mass spectrometry analysis, which agrees with our previous NMR study. The crystal structure of the mutant with the catalytic residue Tyr-136 substituted with alanine shows changes in the position of Ile-74 and Ser-75. This probably altered the binding of the nicotinamide end of NAD(+), which was not visible in the electron density map. The structures presented provide novel insights into cofactor and substrate binding and the reaction mechanism of AtUdh. This information can be applied to the design of efficient microbial conversion of D-galacturonic acid-based waste materials.


    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
Uronate dehydrogenase
A, B, C
267Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Gene Names: udh
EC: 1.1.1.203
Find proteins for Q7CRQ0 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q7CRQ0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
15L
Query on 15L

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Download CCD File 
A, B, C
galactaro-1,5-lactone
(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-oxidotetrahydro-2H-pyran-2-carboxylate
C6 H8 O7
YLKFQNUGXOLRNI-KXMYSMCESA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B, C
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.157 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 165.390α = 90.00
b = 165.390β = 90.00
c = 173.630γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-17
    Type: Database references