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Hydrolase PDB id
1tg7
Jmol
Contents
Protein chain
971 a.a. *
Ligands
NAG-NAG-BMA
NAG ×2
NAG-NAG-BMA-BMA-
MAN-MAN-MAN-MAN-
MAN
NAG-NAG
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN
PO4 ×4
EDO ×9
Metals
_NA ×3
Waters ×1252
* Residue conservation analysis
PDB id:
1tg7
Name: Hydrolase
Title: Native structure of beta-galactosidase from penicillium sp.
Structure: Beta-galactosidase. Chain: a. Synonym: glycosidase family 35. Ec: 3.2.1.23
Source: Penicillium sp.. Organism_taxid: 5081
Biol. unit: Monomer (from PQS)
Resolution:
1.90Å     R-factor:   0.166     R-free:   0.185
Authors: A.L.Rojas,R.A.P.Nagem,K.N.Neustroev,M.Arand,M.Adamska,E.V.En A.A.Kulminskaya,R.C.Garratt,A.M.Golubev,I.Polikarpov
Key ref:
A.L.Rojas et al. (2004). Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. J Mol Biol, 343, 1281-1292. PubMed id: 15491613 DOI: 10.1016/j.jmb.2004.09.012
Date:
28-May-04     Release date:   02-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q700S9  (BGALA_PENSQ) -  Probable beta-galactosidase A
Seq:
Struc: 		 
Seq:
Struc: 		1011 a.a.
971 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.23  - Beta-galactosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1016/j.jmb.2004.09.012 J Mol Biol 343:1281-1292 (2004)
PubMed id: 15491613  
 
 
Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose.
A.L.Rojas, R.A.Nagem, K.N.Neustroev, M.Arand, M.Adamska, E.V.Eneyskaya, A.A.Kulminskaya, R.C.Garratt, A.M.Golubev, I.Polikarpov.
 
  ABSTRACT  
 
Beta-galactosidases catalyze the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and transglycosylation. Here we report the crystallographic structures of Penicillium sp. beta-galactosidase and its complex with galactose solved by the SIRAS quick cryo-soaking technique at 1.90 A and 2.10 A resolution, respectively. The amino acid sequence of this 120 kDa protein was first assigned putatively on the basis of inspection of the experimental electron density maps and then determined by nucleotide sequence analysis. Primary structure alignments reveal that Penicillium sp. beta-galactosidase belongs to family 35 of glycosyl hydrolases (GHF-35). This model is the first 3D structure for a member of GHF-35. Five distinct domains which comprise the structure are assembled in a way previously unobserved for beta-galactosidases. Superposition of this complex with other beta-galactosidase complexes from several hydrolase families allowed the identification of residue Glu200 as the proton donor and residue Glu299 as the nucleophile involved in catalysis. Penicillium sp. beta-galactosidase is a glycoprotein containing seven N-linked oligosaccharide chains and is the only structure of a glycosylated beta-galactosidase described to date.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereo view representation of the galactose-protein interactions in the catalytic site of Psp-b-gal. The galactose molecule is superimposed with an omit electron density map (mF[obs] -DF[calc], f[calc]) contoured at 3 sigma. 		Figure 5.
Figure 5. (a) Stereo view of the superposition of the catalytic sites in Psp-b-gal (in cyan), Ec-b-gal (in orange) and A4-b-gal (in brown). (b) Detailed view of the active site showing the orientation of the aromatic rings of Tyr343 (Psp-b-gal), Phe350 (A4-b-gal) and Trp568 (Ec-b-gal) with respect to the bound galactose. In both pictures only the galactose from the Psp-b-gal complex is shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 1281-1292) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21130883 M.Maksimainen, N.Hakulinen, J.M.Kallio, T.Timoharju, O.Turunen, and J.Rouvinen (2011).
Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site.
  J Struct Biol, 174, 156-163.
PDB codes: 3og2 3ogr 3ogs 3ogv
20496147 X.Hu, S.Robin, S.O'Connell, G.Walsh, and J.G.Wall (2010).
Engineering of a fungal beta-galactosidase to remove product inhibition by galactose.
  Appl Microbiol Biotechnol, 87, 1773-1782.  
18996897 A.L.Cuff, I.Sillitoe, T.Lewis, O.C.Redfern, R.Garratt, J.Thornton, and C.A.Orengo (2009).
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
  Nucleic Acids Res, 37, D310-D314.  
18664295 W.Tanthanuch, M.Chantarangsee, J.Maneesan, and J.Ketudat-Cairns (2008).
Genomic and expression analysis of glycosyl hydrolase family 35 genes from rice (Oryza sativa L.).
  BMC Plant Biol, 8, 84.  
17381511 C.Gamauf, M.Marchetti, J.Kallio, T.Puranen, J.Vehmaanperä, G.Allmaier, C.P.Kubicek, and B.Seiboth (2007).
Characterization of the bga1-encoded glycoside hydrolase family 35 beta-galactosidase of Hypocrea jecorina with galacto-beta-D-galactanase activity.
  FEBS J, 274, 1691-1700.  
15998733 R.Chakrabarti, A.M.Klibanov, and R.A.Friesner (2005).
Computational prediction of native protein ligand-binding and enzyme active site sequences.
  Proc Natl Acad Sci U S A, 102, 10153-10158.  
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.