Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily

Experimental Data Snapshot

  • Resolution: 1.63 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Structure-Function Analysis of 2-Keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate Phosphatase Defines Specificity Elements in Type C0 Haloalkanoate Dehalogenase Family Members.

Lu, Z.Wang, L.Dunaway-Mariano, D.Allen, K.N.

(2009) J Biol Chem 284: 1224-1233

  • DOI: https://doi.org/10.1074/jbc.M807056200
  • Primary Citation of Related Structures:  
    3E81, 3E84, 3E8M

  • PubMed Abstract: 

    The phosphotransferases of the haloalkanoate dehalogenase superfamily (HADSF) act upon a wide range of metabolites in all eukaryotes and prokaryotes and thus constitute a significant force in cell function. The challenge posed for biochemical function assignment of HADSF members is the identification of the structural determinants that target a specific metabolite. The "8KDOP" subfamily of the HADSF is defined by the known structure and catalytic activity of 2-keto-3-deoxy-8-phospho-d-manno-octulosonic acid (KDO-8-P) phosphatase. Homologues of this enzyme have been uniformly annotated as KDO-8-P phosphatase. One such gene, BT1713, from the Bacteroides thetaiotaomicron genome was recently found to encode the enzyme 2-keto-3-deoxy-d-glycero-d-galacto-9-phosphonononic acid (KDN-9-P) phosphatase in the biosynthetic pathway of the 9-carbon alpha-keto acid, 2-keto-3-deoxy-d-glycero-d-galactonononic acid (KDN). To find the structural elements that provide substrate-specific interactions and to allow identification of genomic sequence markers, the x-ray crystal structures of BT1713 liganded to the cofactor Mg(2+)and complexed with tungstate or VO(3)(-)/Neu5Ac were determined to 1.1, 1.85, and 1.63 A resolution, respectively. The structures define the active site to be at the subunit interface and, as confirmed by steady-state kinetics and site-directed mutagenesis, reveal Arg-64(*), Lys-67(*), and Glu-56 to be the key residues involved in sugar binding that are essential for BT1713 catalytic function. Bioinformatic analyses of the differentially conserved residues between BT1713 and KDO-8-P phosphatase homologues guided by the knowledge of the structure-based specificity determinants define Glu-56 and Lys-67(*) to be the key residues that can be used in future annotations.

  • Organizational Affiliation

    Department of Chemistry, Boston University, Boston, Massachusetts 02215-2521, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acylneuraminate cytidylyltransferase
A, B, C, D
164Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: BT_1713
Find proteins for Q8A712 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A712 
Go to UniProtKB:  Q8A712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A712
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SLB

Download Ideal Coordinates CCD File 
K [auth A],
Q [auth B],
R [auth C],
X [auth D]
N-acetyl-beta-neuraminic acid
C11 H19 N O9
Query on PEG

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AA [auth D]
F [auth A]
M [auth B]
N [auth B]
T [auth C]
AA [auth D],
F [auth A],
M [auth B],
N [auth B],
T [auth C],
Z [auth D]
C4 H10 O3
Query on VN4

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BA [auth D],
J [auth A],
P [auth B],
W [auth C]
O3 V
Query on EDO

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G [auth A]
H [auth A]
I [auth A]
O [auth B]
U [auth C]
G [auth A],
H [auth A],
I [auth A],
O [auth B],
U [auth C],
V [auth C]
C2 H6 O2
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
S [auth C],
Y [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.63 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.958α = 90
b = 106.602β = 90
c = 74.83γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-31
    Changes: Refinement description
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary