2VZT

Complex of Amycolatopsis orientalis exo-chitosanase CsxA E541A with PNP-beta-D-glucosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The Structural Basis of Substrate Recognition in an Exo-Beta-D-Glucosaminidase Involved in Chitosan Hydrolysis.

Lammerts Van Bueren, A.Ghinet, M.G.Gregg, K.Fleury, A.Brzezinski, R.Boraston, A.B.

(2009) J Mol Biol 385: 131

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.031
  • Primary Citation of Related Structures:  
    2VZO, 2VZT, 2VZU, 2VZV

  • PubMed Abstract: 

    Family 2 of the glycoside hydrolase classification is one of the largest families. Structurally characterized members of this family include enzymes with beta-galactosidase activity (Escherichia coli LacZ), beta-glucuronidase activity (Homo sapiens GusB), and beta-mannosidase activity (Bacteroides thetaiotaomicron BtMan2A). Here, we describe the structure of a family 2 glycoside hydrolase, CsxA, from Amycolatopsis orientalis that has exo-beta-D-glucosaminidase (exo-chitosanase) activity. Analysis of a product complex (1.85 A resolution) reveals a unique negatively charged pocket that specifically accommodates the nitrogen of nonreducing end glucosamine residues, allowing this enzyme to discriminate between glucose and glucosamine. This also provides structural evidence for the role of E541 as the catalytic nucleophile and D469 as the catalytic acid/base. The structures of an E541A mutant in complex with a natural beta-1,4-D-glucosamine tetrasaccharide substrate and both E541A and D469A mutants in complex with a pNP-beta-D-glucosaminide synthetic substrate provide insight into interactions in the +1 subsite of this enzyme. Overall, a comparison with the active sites of other GH2 enzymes highlights the unique architecture of the CsxA active site, which imparts specificity for its cationic substrate.


  • Organizational Affiliation

    Biochemistry and Microbiology, University of Victoria, BC, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EXO-BETA-D-GLUCOSAMINIDASE
A, B
1,032Amycolatopsis orientalisMutation(s): 1 
UniProt
Find proteins for Q56F26 (Amycolatopsis orientalis)
Explore Q56F26 
Go to UniProtKB:  Q56F26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56F26
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNJ
Query on PNJ

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
4-nitrophenyl 2-amino-2-deoxy-beta-D-glucopyranoside
C12 H16 N2 O7
ZRNBGANFPXCMFT-LZQZFOIKSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth B]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.69α = 90
b = 122.23β = 90.52
c = 91.86γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-10-23
    Changes: Advisory, Data collection, Experimental preparation, Non-polymer description, Other, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary