PDBsum entry 3a23

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
614 a.a. *
GAL ×3
GOL ×19
1PG ×2
SO4 ×5
Waters ×1487
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of beta-l-arabinopyranosidase complexed wi galactose
Structure: Putative secreted alpha-galactosidase. Chain: a, b. Fragment: unp residues 45-658. Engineered: yes
Source: Streptomyces avermitilis. Organism_taxid: 33903. Strain: nbrc14893. Gene: agaa2, sav2186, sav_2186. Expressed in: streptomyces lividans. Expression_system_taxid: 1916.
1.90Å     R-factor:   0.144     R-free:   0.177
Authors: Z.Fujimoto,H.Ichinose,S.Kaneko
Key ref:
H.Ichinose et al. (2009). A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27. J Biol Chem, 284, 25097-25106. PubMed id: 19608743 DOI: 10.1074/jbc.M109.022723
27-Apr-09     Release date:   14-Jul-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q82L26  (Q82L26_STRAW) -  Alpha-galactosidase
658 a.a.
614 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

      Cofactor: Mg(2+); NAD(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  


DOI no: 10.1074/jbc.M109.022723 J Biol Chem 284:25097-25106 (2009)
PubMed id: 19608743  
A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27.
H.Ichinose, Z.Fujimoto, M.Honda, K.Harazono, Y.Nishimoto, A.Uzura, S.Kaneko.
Arabinogalactan proteins (AGPs) are a family of plant cell surface proteoglycans and are considered to be involved in plant growth and development. Because AGPs are very complex molecules, glycoside hydrolases capable of degrading AGPs are powerful tools for analyses of the AGPs. We previously reported such enzymes from Streptomyces avermitilis. Recently, a beta-l-arabinopyranosidase was purified from the culture supernatant of the bacterium, and its corresponding gene was identified. The primary structure of the protein revealed that the catalytic module was highly similar to that of glycoside hydrolase family 27 (GH27) alpha-d-galactosidases. The recombinant protein was successfully expressed as a secreted 64-kDa protein using a Streptomyces expression system. The specific activity toward p-nitrophenyl-beta-l-arabinopyranoside was 18 micromol of arabinose/min/mg, which was 67 times higher than that toward p- nitrophenyl-alpha-d-galactopyranoside. The enzyme could remove 0.1 and 45% l-arabinose from gum arabic or larch arabinogalactan, respectively. X-ray crystallographic analysis reveals that the protein had a GH27 catalytic domain, an antiparallel beta-domain containing Greek key motifs, another antiparallel beta-domain forming a jellyroll structure, and a carbohydrate-binding module family 13 domain. Comparison of the structure of this protein with that of alpha-d-galactosidase showed a single amino acid substitution (aspartic acid to glutamic acid) in the catalytic pocket of beta-l-arabinopyranosidase, and a space for the hydroxymethyl group on the C-5 carbon of d-galactose bound to alpha-galactosidase was changed in beta-l-arabinopyranosidase. Mutagenesis study revealed that the residue is critical for modulating the enzyme activity. This is the first report in which beta-l-arabinopyranosidase is classified as a new member of the GH27 family.
  Selected figure(s)  
Figure 3.
The F[obs] − F[calc] electron density maps contoured at 3 σ for the l-arabinose (A) and galactose (B) molecules bound in the catalytic pocket in the sugar complex structures. Carbon atoms are numbered.
Figure 4.
A, structure of the catalytic pocket of SaArap27A in the l-arabinose complex structure. Hydrogen bonds between SaArap27A and bound l-arabinose (Arap) and glycerol (Gal) are shown as a dashed cyan line. B, structure of the catalytic pocket of SaArap27A in the galactose complex. C, superimposition of the catalytic pocket between SaArap27A (blue) and rice α-galactosidase (brown, PDB entry 1UAS). D, structure of the l- arabinose-binding pocket in the subdomain α of SaArap27A domain IV in the l-arabinose complex structure. Hydrogen bonds between SaArap27A and the bound l-arabinose are shown as a dashed cyan line. E and F, l-arabinose binding pocket in subdomains β and γ of SaArap27A domain IV in the l-arabinose complex structure.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 25097-25106) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20933404 S.Kühnel, Y.Westphal, S.W.Hinz, H.A.Schols, and H.Gruppen (2011).
Mode of action of Chrysosporium lucknowense C1 α-l-arabinohydrolases.
  Bioresour Technol, 102, 1636-1643.  
19809163 Z.Fujimoto, S.Kaneko, W.D.Kim, G.G.Park, M.Momma, and H.Kobayashi (2009).
The tetramer structure of the glycoside hydrolase family 27 alpha-galactosidase I from Umbelopsis vinacea.
  Biosci Biotechnol Biochem, 73, 2360-2364.
PDB code: 3a5v
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.