2EPN

N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

Langley, D.B.Harty, D.W.S.Jacques, N.A.Hunter, N.Guss, J.M.Collyer, C.A.

(2008) J Mol Biol 377: 104-116

  • DOI: https://doi.org/10.1016/j.jmb.2007.09.028
  • Primary Citation of Related Structures:  
    2EPK, 2EPL, 2EPM, 2EPN, 2EPO

  • PubMed Abstract: 

    The crystal structure of GcnA, an N-acetyl-beta-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal alpha-helical domain has not been observed previously and forms a large dimerisation interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical (beta/alpha)(8) TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a family 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-beta-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.


  • Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyl-beta-D-glucosaminidase
A, B
627Streptococcus gordoniiMutation(s): 0 
Gene Names: gcna
EC: 3.2.1.52
UniProt
Find proteins for Q6ST21 (Streptococcus gordonii)
Explore Q6ST21 
Go to UniProtKB:  Q6ST21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ST21
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGT
Query on NGT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NGT PDBBind:  2EPN Ki: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.574α = 90
b = 112.332β = 90
c = 103.127γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description