2BKX

Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Kinetics of a Monomeric Glucosamine 6-Phosphate Deaminase: Missing Link of the Nagb Superfamily?

Vincent, F.Davies, G.J.Brannigan, J.A.

(2005) J.Biol.Chem. 280: 19649

  • DOI: 10.1074/jbc.M502131200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glucosamine 6-phosphate is converted to fructose 6-phosphate and ammonia by the action of the enzyme glucosamine 6-phosphate deaminase, NagB. This reaction is the final step in the specific GlcNAc utilization pathway and thus decides the metabolic fa ...

    Glucosamine 6-phosphate is converted to fructose 6-phosphate and ammonia by the action of the enzyme glucosamine 6-phosphate deaminase, NagB. This reaction is the final step in the specific GlcNAc utilization pathway and thus decides the metabolic fate of GlcNAc. Sequence analyses suggest that the NagB "superfamily" consists of three main clusters: multimeric and allosterically regulated glucosamine-6-phosphate deaminases (exemplified by Escherichia coli NagB), phosphogluconolactonases, and monomeric hexosamine-6-phosphate deaminases. Here we present the three-dimensional structure and kinetics of the first member of this latter group, the glucosamine-6-phosphate deaminase, NagB, from Bacillus subtilis. The structures were determined in ligand-complexed forms at resolutions around 1.4 Angstroms. BsuNagB is monomeric in solution and as a consequence is active (k(cat) 28 s(-1), K(m(app)) 0.13 mM) without the need for allosteric activators. A decrease in activity at high substrate concentrations may reflect substrate inhibition (with K(i) of approximately 4 mM). The structure completes the NagB superfamily structural landscape and thus allows further interrogation of genomic data in terms of the regulation of NagB and the metabolic fate(s) of glucosamine 6-phosphate.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSAMINE-6-PHOSPHATE DEAMINASE
A, B
242Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: nagB
EC: 3.5.99.6
Find proteins for O35000 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O35000
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F6R
Query on F6R

Download SDF File 
Download CCD File 
A, B
FRUCTOSE -6-PHOSPHATE
C6 H13 O9 P
GSXOAOHZAIYLCY-HSUXUTPPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.119 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.966α = 90.00
b = 47.898β = 90.06
c = 71.397γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance