1UAS

Crystal structure of rice alpha-galactosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of rice alpha-galactosidase complexed with D-galactose

Fujimoto, Z.Kaneko, S.Momma, M.Kobayashi, H.Mizuno, H.

(2003) J.Biol.Chem. 278: 20313-20318

  • DOI: 10.1074/jbc.M302292200

  • PubMed Abstract: 
  • alpha-Galactosidases catalyze the hydrolysis of alpha-1,6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto-(gluco)mannans. The crystal structure of rice alpha-galactosidase has been determined at 1.5A resolution using th ...

    alpha-Galactosidases catalyze the hydrolysis of alpha-1,6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto-(gluco)mannans. The crystal structure of rice alpha-galactosidase has been determined at 1.5A resolution using the multiple isomorphous replacement method. The structure consisted of a catalytic domain and a C-terminal domain and was essentially the same as that of alpha-N-acetylgalactosaminidase, which is the same member of glycosyl hydrolase family 27. The catalytic domain had a (beta/alpha)8-barrel structure, and the C-terminal domain was made up of eight beta-strands containing a Greek key motif. The structure was solved as a complex with d-galactose, providing a mode of substrate binding in detail. The d-galactose molecule was found bound in the active site pocket on the C-terminal side of the central beta-barrel of the catalytic domain. The d-galactose molecule consisted of a mixture of two anomers present in a ratio equal to their natural abundance. Structural comparisons of rice alpha-galactosidase with chicken alpha-N-acetylgalactosaminidase provided further understanding of the substrate recognition mechanism in these enzymes.


    Related Citations: 
    • alpha-Galactosidase from cultured rice (Oryza sativa L. var. Nipponbare) cells
      Kim, W.,Kobayashi, O.,Kaneko, S.,Sakakibara, Y.,Park, G.,Kusakabe, I.,Tanaka, H.,Kobayashi, H.
      (2002) PHYTOCHEMISTRY 61: 621
    • Crystallization and preliminary X-ray crystallographic studies of rice alpha-galactosidase
      Fujimoto, Z.,Kobayashi, O.,Kaneko, S.,Momma, M.,Kobayashi, H.,Mizuno, H.
      (2002) Acta Crystallogr.,Sect.D 58: 1374


    Organizational Affiliation

    Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha-galactosidase
A
362Oryza sativa subsp. japonicaMutation(s): 0 
EC: 3.2.1.22
Find proteins for Q9FXT4 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q9FXT4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PT
Query on PT

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Download CCD File 
A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.656α = 90.00
b = 71.420β = 90.00
c = 86.238γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MLPHAREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance