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Hydrolase PDB id
1yq2
Jmol
Contents
Protein chains
(+ 0 more) 1020 a.a. *
Ligands
SO4 ×11
PEG ×6
Metals
_MG ×6
_NA ×12
_CL ×6
Waters ×6471
* Residue conservation analysis
PDB id:
1yq2
Name: Hydrolase
Title: Beta-galactosidase from arthrobacter sp. C2-2 (isoenzyme c2- 2-1)
Structure: Beta-galactosidase. Chain: a, b, c, d, e, f. Engineered: yes. Mutation: yes
Source: Arthrobacter sp. C2-2. Organism_taxid: 192168. Gene: lacz. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
1.90Å     R-factor:   0.157     R-free:   0.195
Authors: T.Skalova,J.Dohnalek,V.Spiwok,P.Lipovova,E.Vondrackova, H.Petrokova,H.Strnad,B.Kralova,J.Hasek
Key ref:
T.Skálová et al. (2005). Cold-active beta-galactosidase from Arthrobacter sp. C2-2 forms compact 660 kDa hexamers: crystal structure at 1.9A resolution. J Mol Biol, 353, 282-294. PubMed id: 16171818 DOI: 10.1016/j.jmb.2005.08.028
Date:
01-Feb-05     Release date:   04-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8KRF6  (Q8KRF6_9MICC) -  Beta-galactosidase
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1023 a.a.
1020 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.3.2.1.23  - 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     beta-galactosidase complex   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
DOI no: 10.1016/j.jmb.2005.08.028 J Mol Biol 353:282-294 (2005)
PubMed id: 16171818  
 
 
Cold-active beta-galactosidase from Arthrobacter sp. C2-2 forms compact 660 kDa hexamers: crystal structure at 1.9A resolution.
T.Skálová, J.Dohnálek, V.Spiwok, P.Lipovová, E.Vondrácková, H.Petroková, J.Dusková, H.Strnad, B.Králová, J.Hasek.
 
  ABSTRACT  
 
The X-ray structure of cold-active beta-galactosidase (isoenzyme C-2-2-1) from an Antarctic bacterium Arthrobacter sp. C2-2 was solved at 1.9A resolution. The enzyme forms 660 kDa hexamers with active sites opened to the central cavity of the hexamer and connected by eight channels with exterior solvent. To our best knowledge, this is the first cold-active beta-galactosidase with known structure and also the first known beta-galactosidase structure in the form of compact hexamers. The hexamer organization regulates access of substrates and ligands to six active sites and this unique packing, present also in solution, raises questions about its purpose and function. This enzyme belongs to glycosyl hydrolase family 2, similarly to Escherichia coli beta-galactosidase, forming tetramers necessary for its enzymatic function. However, we discovered significant differences between these two enzymes affecting the ability of tetramer/hexamer formation and complementation of the active site. This structure reveals new insights into the cold-adaptation mechanisms of enzymatic pathways of extremophiles.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. A cross-section of the hexamer of b-galactosidase from Arthrobacter sp. C2-2 (cutting plane in black). The inner cavity is connected with exterior space by eight channels of three types, I, II and III. Five of the channels can be seen here. The active sites of all monomers are opened into this inner cavity. The cavity is partly filled by localized water molecules (yellow spheres). The colouring scheme of monomers is the same as in Figure 3. The Figure was prepared in INSIGHTII (Accelrys). 		Figure 5.
Figure 5. Surface contact regions of monomer A in (a) the hexamer of C221-b-Gal and (b) the tetramer of EC-b-Gal, both in the same orientation of the monomer A. The active site residues are in green: Glu442, Glu521, Trp552 and Cys999 (C221-b-Gal); Glu461, Glu537, Trp568 and Trp999 (EC-b-Gal). The capital letters mark the surface areas (distinguished by different colouring) involved in contacts with the corresponding monomers. The solvent-accessible surface was coloured on the basis of non-zero contact area of a given atom (program AREAIMOL in CCP423). (c) Comparison of monomer A placing in the hexamer of C221-b-Gal and the tetramer of EC-b-Gal, using the same colouring scheme as for surface contacts in (a) and (b). The Figure was prepared in INSIGHTII (Accelrys).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 282-294) copyright 2005.  
  Figures were selected by the author.  

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
20713699 A.Sandberg, L.M.Luheshi, S.Söllvander, T.Pereira de Barros, B.Macao, T.P.Knowles, H.Biverstål, C.Lendel, F.Ekholm-Petterson, A.Dubnovitsky, L.Lannfelt, C.M.Dobson, and T.Härd (2010).
Stabilization of neurotoxic Alzheimer amyloid-beta oligomers by protein engineering.
  Proc Natl Acad Sci U S A, 107, 15595-15600.  
20077037 J.Krahulec, T.Szemes, and J.Krahulcová (2010).
Bioinformatics characterization of potential new beta-glucuronidase from Streptococcus equi subsp. zooepidemicus.
  Mol Biotechnol, 44, 232-241.  
19376973 A.K.Paravastu, I.Qahwash, R.D.Leapman, S.C.Meredith, and R.Tycko (2009).
Seeded growth of beta-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure.
  Proc Natl Acad Sci U S A, 106, 7443-7448.  
19706519 B.Chen, K.R.Thurber, F.Shewmaker, R.B.Wickner, and R.Tycko (2009).
Measurement of amyloid fibril mass-per-length by tilted-beam transmission electron microscopy.
  Proc Natl Acad Sci U S A, 106, 14339-14344.  
19631003 P.Hildebrandt, M.Wanarska, and J.Kur (2009).
A new cold-adapted beta-D-galactosidase from the Antarctic Arthrobacter sp. 32c - gene cloning, overexpression, purification and properties.
  BMC Microbiol, 9, 151.  
19264960 R.Zhang, X.Hu, H.Khant, S.J.Ludtke, W.Chiu, M.F.Schmid, C.Frieden, and J.M.Lee (2009).
Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM.
  Proc Natl Acad Sci U S A, 106, 4653-4658.  
19015532 A.K.Paravastu, R.D.Leapman, W.M.Yau, and R.Tycko (2008).
Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils.
  Proc Natl Acad Sci U S A, 105, 18349-18354.  
17287210 L.E.Tailford, V.A.Money, N.L.Smith, C.Dumon, G.J.Davies, and H.J.Gilbert (2007).
Mannose foraging by Bacteroides thetaiotaomicron: structure and specificity of the beta-mannosidase, BtMan2A.
  J Biol Chem, 282, 11291-11299.
PDB code: 2je8
17548239 M.Ferrer, O.Golyshina, A.Beloqui, and P.N.Golyshin (2007).
Mining enzymes from extreme environments.
  Curr Opin Microbiol, 10, 207-214.  
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.