3A5V

Crystal structure of alpha-galactosidase I from Mortierella vinacea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

wwPDB Validation 3D Report Full Report



Literature

The Tetramer Structure of the Glycoside Hydrolase Family 27 alpha-Galactosidase I from Umbelopsis vinacea

Fujimoto, Z.Kaneko, S.Kim, W.-D.Park, G.-G.Momma, M.Kobayashi, H.

(2009) Biosci Biotechnol Biochem 73: 2360-2364

  • DOI: 10.1271/bbb.90604
  • Primary Citation of Related Structures:  
    3A5V

  • PubMed Abstract: 
  • The crystal structure of Umbelopsis vinacea alpha-galactosidase I, which belongs to glycoside hydrolase family 27, was determined at 2.0 A resolution. The monomer structure was well conserved with those of glycoside hydrolase family 27 enzymes. The b ...

    The crystal structure of Umbelopsis vinacea alpha-galactosidase I, which belongs to glycoside hydrolase family 27, was determined at 2.0 A resolution. The monomer structure was well conserved with those of glycoside hydrolase family 27 enzymes. The biological tetramer structure of this enzyme was constructed by the crystallographic 4-fold symmetry, and tetramerization appeared to be caused by three inserted peptides that were involved in the tetramer interface. The quaternary structure indicated that the substrate specificity of this enzyme might be related to the tetramer formation. Three N-glycosylated sugar chains were observed, and their structures were found to be of the high-mannose type.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic studies of alpha-galactosidase I from Mortierella vinacea
      Fujimoto, Z., Kim, W.-D., Kaneko, S., Park, G.-G., Momma, M., Kobayashi, H., Mizuno, H.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 2289
    • Purification, characterization, and cDNA cloning of a novel alpha-galactosidase from Mortierella vinacea
      Shibuya, H., Kobayashi, H., Sato, T., Kim, W.S., Yoshida, S., Kaneko, S., Kasamo, K., Kusakabe, I.
      (1997) Biosci Biotechnol Biochem 61: 592

    Organizational Affiliation

    Protein Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan. zui@affrc.go.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-galactosidaseA397Umbelopsis vinaceaMutation(s): 0 
EC: 3.2.1.22
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
7 N-Glycosylation
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download CCD File 
A
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.47α = 90
b = 142.47β = 90
c = 130.58γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DPSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary