4U6D

Zg3615, a family 117 glycoside hydrolase in complex with beta-3,6-anhydro-L-galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family.

Ficko-Blean, E.Duffieux, D.Rebuffet, E.Larocque, R.Groisillier, A.Michel, G.Czjzek, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 209-223

  • DOI: https://doi.org/10.1107/S1399004714025024
  • Primary Citation of Related Structures:  
    4U6B, 4U6D

  • PubMed Abstract: 

    The family 117 glycoside hydrolase (GH117) enzymes have exo-α-1,3-(3,6-anhydro)-L-galactosidase activity, removing terminal nonreducing α-1,3-linked 3,6-anhydro-L-galactose residues from their red algal neoagarose substrate. These enzymes have previously been phylogenetically divided into clades, and only the clade A enzymes have been experimentally studied to date. The investigation of two GH117 enzymes, Zg3615 and Zg3597, produced by the marine bacterium Zobellia galactanivorans reveals structural, biochemical and further phylogenetic diversity between clades. A product complex with the unusual β-3,6-anhydro-L-galactose residue sheds light on the inverting catalytic mechanism of the GH117 enzymes as well as the structure of this unique sugar produced by hydrolysis of the agarophyte red algal cell wall.


  • Organizational Affiliation

    Sorbonne Universités, UPMC Université Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff CEDEX, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved hypothetical periplasmic protein
A, B
414Zobellia galactanivoransMutation(s): 0 
Gene Names: zobellia_3615
EC: 3.2.1
UniProt
Find proteins for F0V1E2 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore F0V1E2 
Go to UniProtKB:  F0V1E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF0V1E2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3DY
Query on 3DY

Download Ideal Coordinates CCD File 
W [auth A]3,6-anhydro-beta-L-galactopyranose
C6 H10 O5
DCQFFOLNJVGHLW-ZSNZIGRDSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
F [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
X [auth B],
Y [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.109α = 90
b = 226.132β = 90
c = 67.124γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description