Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans

Experimental Data Snapshot

  • Resolution: 2.03 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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Ring-opening mechanism revealed by crystal structures of NagB and its ES intermediate complex

Liu, C.Li, D.Liang, Y.H.Li, L.F.Su, X.D.

(2008) J Mol Biol 379: 73-81

  • DOI: https://doi.org/10.1016/j.jmb.2008.03.031
  • Primary Citation of Related Structures:  
    2RI0, 2RI1

  • PubMed Abstract: 

    Glucosamine 6-phosphate deaminase (NagB) catalyzes the conversion of d-glucosamine 6-phosphate (GlcN6P) to d-fructose 6-phosphate and ammonia. This reaction is the final step of N-acetylglucosamine utilization and decides its metabolic fate. The enzyme from Streptococcus mutans belongs to the monomeric subfamily of NagB. The crystal structure of the native SmuNagB (NagB from S. mutans) presented here, compared with the structures of its homologs BsuNagB (NagB from Bacillus subtilis) and EcoNagB (NagB from E. coli), implies a conformational change of the 'lid' motif in the activation of the monomeric NagB enzyme. We have also captured the enzyme-substrate intermediate complex of the NagB family at low pH, where a remarkable loss of the catalytic activity of SmuNagB was detected. The enzyme-substrate intermediate presents the initial step of the GlcN6P deaminase reaction. The structural evidence (1) supports the alpha-anomer of GlcN6P as the specific natural substrate of NagB; (2) displays the substrate-binding pocket at the active site; and (3) together with the site-directed mutagenesis studies, demonstrates the ring-opening mechanism of an Asn-His-Glu triad that performs the proton transfer from O1 to O5 to open the sugar ring.

  • Organizational Affiliation

    National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosamine-6-phosphate deaminase
A, B
235Streptococcus mutansMutation(s): 0 
Gene Names: SMU.636
Find proteins for Q8DV70 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q8DV70 
Go to UniProtKB:  Q8DV70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DV70
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.03 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.92α = 90
b = 82.48β = 90
c = 135.28γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Structure summary