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PDBsum entry 3lrl

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protein ligands metals links
Hydrolase PDB id
3lrl
Jmol
Contents
Protein chain
452 a.a. *
Ligands
NAG ×4
NAG-NAG ×2
GLC-GLA
Metals
_NA
Waters ×415
* Residue conservation analysis
PDB id:
3lrl
Name: Hydrolase
Title: Structure of alfa-galactosidase (mel1) from saccharomyces ce with melibiose
Structure: Alpha-galactosidase 1. Chain: a. Synonym: alpha-d-galactoside galactohydrolase 1, melibiase engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Gene: mel1. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
2.40Å     R-factor:   0.201     R-free:   0.253
Authors: R.Fernandez-Leiro,A.Pereira-Rodriguez,M.E.Cerdan,M.Becerra,J Aparicio
Key ref: R.Fernández-Leiro et al. (2010). Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases. J Biol Chem, 285, 28020-28033. PubMed id: 20592022 DOI: 10.1074/jbc.M110.144584
Date:
11-Feb-10     Release date:   30-Jun-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04824  (MEL1_YEASX) -  Alpha-galactosidase 1
Seq:
Struc:
471 a.a.
452 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.22  - Alpha-galactosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Melibiose + H2O = galactose + glucose

+
=
+
      Cofactor: Mg(2+); NAD(+)
Mg(2+)
NAD(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M110.144584 J Biol Chem 285:28020-28033 (2010)
PubMed id: 20592022  
 
 
Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases.
R.Fernández-Leiro, A.Pereira-Rodríguez, M.E.Cerdán, M.Becerra, J.Sanz-Aparicio.
 
  ABSTRACT  
 
a-Galactosidases catalyze the hydrolysis of terminal a-1,6-galactosyl units from galacto-oligosaccharides and polymeric galactomannans. The crystal structures of tetrameric Saccharomyces cerevisiae a-galactosidase and its complexes with the substrates melibiose and raffinose have been determined to 1.95, 2.40 and 2.70 A resolution. The monomer folds into a catalytic (a/b)8 barrel and a C-terminal b-sandwich domain with unassigned function. This pattern is conserved with other family 27 glycosidases, but this enzyme presents a unique 45-residues insertion in the b-sandwich domain that folds over the barrel protecting it from the solvent and being likely the reason explaining its high stability. The structure of the complexes and the mutational analysis show that oligomerization is a key factor in substrate binding, as the substrates are located in a deep tunnel making direct interactions with the adjacent subunit. Furthermore, docking analysis suggests that the supplementary domain could be involved in binding sugar units distal from the scissile bond, therefore, ascribing a role in fine-tuning substrate specificity to this domain. It may also have a role in promoting association with the polymeric substrate owing to the ordered arrangement that the four domains presents in one face of the tetramer. Our analysis extends to other family 27 glycosidases, where some traits regarding specificity and oligomerization can be formulated on the basis of their sequence and the structures available. These results improve our knowledge on the activity of this important family of enzymes, and give a deeper insight into the structural features that rule modularity and protein-carbohydrate interactions.