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PDBsum entry 1uas

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protein ligands metals links
Hydrolase PDB id
1uas
Jmol
Contents
Protein chain
362 a.a. *
Ligands
GLA
SO4
GOL ×7
Metals
_PT
Waters ×638
* Residue conservation analysis
PDB id:
1uas
Name: Hydrolase
Title: Crystal structure of rice alpha-galactosidase
Structure: Alpha-galactosidase. Chain: a. Fragment: resiudes 1-362. Engineered: yes
Source: Oryza sativa. Rice. Organism_taxid: 4530. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.50Å     R-factor:   0.160     R-free:   0.178
Authors: Z.Fujimoto,S.Kaneko,M.Momma,H.Kobayashi,H.Mizuno
Key ref:
Z.Fujimoto et al. (2003). Crystal structure of rice alpha-galactosidase complexed with D-galactose. J Biol Chem, 278, 20313-20318. PubMed id: 12657636 DOI: 10.1074/jbc.M302292200
Date:
18-Mar-03     Release date:   01-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9FXT4  (AGAL_ORYSJ) -  Alpha-galactosidase
Seq:
Struc:
417 a.a.
362 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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!
  Cellular component     plant-type cell wall   1 term 
  Biological process     metabolic process   8 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M302292200 J Biol Chem 278:20313-20318 (2003)
PubMed id: 12657636  
 
 
Crystal structure of rice alpha-galactosidase complexed with D-galactose.
Z.Fujimoto, S.Kaneko, M.Momma, H.Kobayashi, H.Mizuno.
 
  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 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.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Stereo view of the ribbon model of rice -galactosidase. The bound D-galactose, two catalytic residues, and two disulfide bonds are indicated by ball-and-stick drawings and shown in black, red, and green, respectively. The figure was drawn with the program Raster3d (39, 40).
Figure 4.
FIG. 4. Stereoview of the F[o] - F[c] omit electron density map for the bound D-galactose and two catalytic residues contoured at 3.5
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 20313-20318) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19940122 A.I.Guce, N.E.Clark, E.N.Salgado, D.R.Ivanen, A.A.Kulminskaya, H.Brumer, and S.C.Garman (2010).
Catalytic mechanism of human alpha-galactosidase.
  J Biol Chem, 285, 3625-3632.
PDB codes: 3hg2 3hg3 3hg4 3hg5
20681989 H.Nakai, M.J.Baumann, B.O.Petersen, Y.Westphal, M.A.Hachem, A.Dilokpimol, J...Duus, H.A.Schols, and B.Svensson (2010).
Aspergillus nidulans alpha-galactosidase of glycoside hydrolase family 36 catalyses the formation of alpha-galacto-oligosaccharides by transglycosylation.
  FEBS J, 277, 3538-3551.  
20714719 J.Zhou, P.Shi, H.Huang, Y.Cao, K.Meng, P.Yang, R.Zhang, X.Chen, and B.Yao (2010).
A new α-galactosidase from symbiotic Flavobacterium sp. TN17 reveals four residues essential for α-galactosidase activity of gastrointestinal bacteria.
  Appl Microbiol Biotechnol, 88, 1297-1309.  
19937437 T.Sakamoto, Y.Tsujitani, K.Fukamachi, Y.Taniguchi, and H.Ihara (2010).
Identification of two GH27 bifunctional proteins with beta-L-arabinopyranosidase/alpha-D-galactopyranosidase activities from Fusarium oxysporum.
  Appl Microbiol Biotechnol, 86, 1115-1124.  
18953653 A.Kumar, N.K.Singhal, B.Ramanujam, A.Mitra, N.R.Rameshwaram, S.K.Nadimpalli, and C.P.Rao (2009).
C(1)-/C(2)-aromatic-imino-glyco-conjugates: experimental and computational studies of binding, inhibition and docking aspects towards glycosidases isolated from soybean and jack bean.
  Glycoconj J, 26, 495-510.  
19608743 H.Ichinose, Z.Fujimoto, M.Honda, K.Harazono, Y.Nishimoto, A.Uzura, and S.Kaneko (2009).
A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27.
  J Biol Chem, 284, 25097-25106.
PDB codes: 3a21 3a22 3a23
19683538 N.E.Clark, and S.C.Garman (2009).
The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.
  J Mol Biol, 393, 435-447.
PDB codes: 3h53 3h54 3h55 3igu
19288093 Y.Cao, Y.Wang, K.Meng, Y.Bai, P.Shi, H.Luo, P.Yang, Z.Zhou, Z.Zhang, and B.Yao (2009).
A novel protease-resistant alpha-galactosidase with high hydrolytic activity from Gibberella sp. F75: gene cloning, expression, and enzymatic characterization.
  Appl Microbiol Biotechnol, 83, 875-884.  
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
18848471 T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, and G.J.Davies (2008).
Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.
  Chem Biol, 15, 1058-1067.
PDB codes: 2jka 2jke 2jkp
17206375 S.Li, T.Li, W.D.Kim, M.Kitaoka, S.Yoshida, M.Nakajima, and H.Kobayashi (2007).
Characterization of raffinose synthase from rice (Oryza sativa L. var. Nipponbare).
  Biotechnol Lett, 29, 635-640.  
17284836 S.Li, W.D.Kim, S.Kaneko, P.A.Prema, M.Nakajima, and H.Kobayashi (2007).
Expression of rice (Oryza sativa L. var. Nipponbare) alpha-galactosidase genes in Escherichia coli and characterization.
  Biosci Biotechnol Biochem, 71, 520-526.  
16842369 M.S.Centeno, C.I.Guerreiro, F.M.Dias, C.Morland, L.E.Tailford, A.Goyal, J.A.Prates, L.M.Ferreira, R.M.Caldeira, E.F.Mongodin, K.E.Nelson, H.J.Gilbert, and C.M.Fontes (2006).
Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus.
  FEMS Microbiol Lett, 261, 123-132.  
16547025 S.J.Brouns, N.Smits, H.Wu, A.P.Snijders, P.C.Wright, W.M.de Vos, and J.van der Oost (2006).
Identification of a novel alpha-galactosidase from the hyperthermophilic archaeon Sulfolobus solfataricus.
  J Bacteriol, 188, 2392-2399.  
16320365 S.W.Hinz, C.H.Doeswijk-Voragen, R.Schipperus, L.A.van den Broek, J.P.Vincken, and A.G.Voragen (2006).
Increasing the transglycosylation activity of alpha-galactosidase from Bifidobacterium adolescentis DSM 20083 by site-directed mutagenesis.
  Biotechnol Bioeng, 93, 122-131.  
16131397 D.G.Naumoff (2005).
GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily.
  BMC Genomics, 6, 112.  
15676072 J.Hujová, J.Sikora, R.Dobrovolný, H.Poupetová, J.Ledvinová, M.Kostrouchová, and M.Hrebícek (2005).
Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate alpha-galactosidase and alpha-N-acetylgalactosaminidase.
  BMC Cell Biol, 6, 5.  
14993697 M.Akita, M.Mizuno, T.Tonozuka, Y.Sakano, H.Matsui, Y.Hidaka, Y.Hatada, S.Ito, and K.Horikoshi (2004).
Crystallization and preliminary X-ray study of isomaltodextranase from Arthrobacter globiformis.
  Acta Crystallogr D Biol Crystallogr, 60, 572-573.  
15604681 R.H.Lee, M.C.Lin, and S.C.Chen (2004).
A novel alkaline alpha-galactosidase gene is involved in rice leaf senescence.
  Plant Mol Biol, 55, 281-295.  
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 codes are shown on the right.