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PDBsum entry 1t0o

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Hydrolase PDB id
1t0o
Jmol
Contents
Protein chain
417 a.a. *
Ligands
NAG-NAG ×2
NAG-NAG-BMA-MAN-
MAN-MAN-MAN
NAG-NAG-BMA-MAN
GAL
Waters ×384
* Residue conservation analysis
PDB id:
1t0o
Name: Hydrolase
Title: The structure of alpha-galactosidase from trichoderma reesei with beta-d-galactose
Structure: Alpha-galactosidase. Chain: a. Ec: 3.2.1.22
Source: Hypocrea jecorina. Organism_taxid: 51453
Resolution:
1.96Å     R-factor:   0.157     R-free:   0.205
Authors: A.M.Golubev,R.A.P.Nagem,J.R.Brandao Neto,K.N.Neustroev,E.V.E A.A.Kulminskaya,K.A.Shabalin,A.N.Savel'Ev,I.Polikarpov
Key ref:
A.M.Golubev et al. (2004). Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism. J Mol Biol, 339, 413-422. PubMed id: 15136043 DOI: 10.1016/j.jmb.2004.03.062
Date:
12-Apr-04     Release date:   12-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q92456  (Q92456_HYPJE) -  Alpha-galactosidase
Seq:
Struc:
444 a.a.
417 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 40 residue positions (black crosses)

 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     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.03.062 J Mol Biol 339:413-422 (2004)
PubMed id: 15136043  
 
 
Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism.
A.M.Golubev, R.A.Nagem, J.R.Brandão Neto, K.N.Neustroev, E.V.Eneyskaya, A.A.Kulminskaya, K.A.Shabalin, A.N.Savel'ev, I.Polikarpov.
 
  ABSTRACT  
 
The crystal structures of alpha-galactosidase from the mesophilic fungus Trichoderma reesei and its complex with the competitive inhibitor, beta-d-galactose, have been determined at 1.54 A and 2.0 A resolution, respectively. The alpha-galactosidase structure was solved by the quick cryo-soaking method using a single Cs derivative. The refined crystallographic model of the alpha-galactosidase consists of two domains, an N-terminal catalytic domain of the (beta/alpha)8 barrel topology and a C-terminal domain which is formed by an antiparallel beta-structure. The protein contains four N-glycosylation sites located in the catalytic domain. Some of the oligosaccharides were found to participate in inter-domain contacts. The galactose molecule binds to the active site pocket located in the center of the barrel of the catalytic domain. Analysis of the alpha-galactosidase- galactose complex reveals the residues of the active site and offers a structural basis for identification of the putative mechanism of the enzymatic reaction. The structure of the alpha-galactosidase closely resembles those of the glycoside hydrolase family 27. The conservation of two catalytic Asp residues, identified for this family, is consistent with a double-displacement reaction mechanism for the alpha-galactosidase. Modeling of possible substrates into the active site reveals specific hydrogen bonds and hydrophobic interactions that could explain peculiarities of the enzyme kinetics.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) Stereo view of the inhibitor, b- Image -galactose, and the a-galactosidase residues participating in binding. The inhibitor is well defined by both (F[o] -F[c]) omit electron density map contoured at 3s (green) and 5s (red). (b) Diagram representing the interactions between enzyme and b-d-galactose. All five hydroxyl groups of galactose participate in hydrogen bonds with residues of the active site. The hydrogen bonds are shown as blue lines, van der Waals contacts are shown as brown lines.
Figure 4.
Figure 4. (a) Stereo view illustrating the role of hydrophobic interactions: The position of PNPG obtained by superposition of the hexose ring with b- Image -galactose (gray) inside the catalytic pocket and its putative rotation caused by the hydrophobic interactions between the nitrophenyl group of the substrate and Trp205. (b) Oxidative activation is caused by a strong interaction between the Asp54 Od2 and a polar SO-group of methionine sulphoxide combined with the release of the Asp54-hexose O-4 hydrogen bond. (c) A model of 1,6-a- Image -galactopyranosyl galactopyranoside fitted into the catalytic pocket.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 413-422) copyright 2004.  
  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
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.  
20601723 N.Kulik, L.Weignerová, T.Filipi, P.Pompach, P.Novák, H.Mrázek, K.Slámová, K.Bezouska, V.Kren, and R.Ettrich (2010).
The α-galactosidase type A gene aglA from Aspergillus niger encodes a fully functional α-N-acetylgalactosaminidase.
  Glycobiology, 20, 1410-1419.  
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.  
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
19005653 T.Goulas, A.Goulas, G.Tzortzis, and G.R.Gibson (2009).
A novel alpha-galactosidase from Bifidobacterium bifidum with transgalactosylating properties: gene molecular cloning and heterologous expression.
  Appl Microbiol Biotechnol, 82, 471-477.  
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
17009317 K.A.Selz, T.I.Samoylova, A.M.Samoylov, V.J.Vodyanoy, and A.J.Mandell (2007).
Designing allosteric peptide ligands targeting a globular protein.
  Biopolymers, 85, 38-59.  
  16511274 M.Foucault, H.Watzlawick, R.Mattes, R.Haser, and P.Gouet (2006).
Crystallization and preliminary X-ray diffraction studies of two thermostable alpha-galactosidases from glycoside hydrolase family 36.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 100-103.  
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.  
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.