3R1X

Crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.

Michalska, K., Cuff, M.E., Tesar, C., Feldmann, B., Joachimiak, A.

(2011) Acta Crystallogr D Biol Crystallogr 67: 678-689

  • DOI: 10.1107/S0907444911021834
  • Primary Citation of Related Structures:  
    3R1X

  • PubMed Abstract: 

    • In most organisms, efficient D-galactose utilization requires the highly conserved Leloir pathway that converts D-galactose to D-glucose 1-phosphate. However, in some bacterial and fungal species alternative routes of D-galactose assimilation have been identified ...

    In most organisms, efficient D-galactose utilization requires the highly conserved Leloir pathway that converts D-galactose to D-glucose 1-phosphate. However, in some bacterial and fungal species alternative routes of D-galactose assimilation have been identified. In the so-called De Ley-Doudoroff pathway, D-galactose is metabolized into pyruvate and D-glyceraldehyde 3-phosphate in five consecutive reactions carried out by specific enzymes. The penultimate step in this pathway involves the phosphorylation of 2-oxo-3-deoxygalactonate to 2-oxo-3-deoxygalactonate 6-phosphate catalyzed by 2-oxo-3-deoxygalactonate kinase, with ATP serving as a phosphoryl-group donor. Here, a crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae determined at 2.1 Å resolution is reported, the first structure of an enzyme from the De Ley-Doudoroff pathway. Structural comparison indicates that the enzyme belongs to the ASKHA (acetate and sugar kinases/hsc70/actin) family of phosphotransferases. The protein is composed of two α/β domains, each of which contains a core common to all family members. Additional elements introduced between conserved structural motifs define the unique features of 2-oxo-3-deoxygalactonate kinase and possibly determine the biological function of the protein.

    Organizational Affiliation: 

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-oxo-3-deoxygalactonate kinaseA, B, C, D295Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 0 
Gene Names: dgoK, KPN78578_40560, KPN_04097
EC: 2.7.1.58
UniProt
Find proteins for A6TFZ6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TFZ6 
Go to UniProtKB:  A6TFZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TFZ6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
R [auth D],
Y [auth D]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.509α = 90
b = 134.026β = 90
c = 139.906γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2011-09-21
    Changes: Other