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PDBsum entry 2x40

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protein ligands metals links
Hydrolase PDB id
2x40
Jmol
Contents
Protein chain
713 a.a. *
Ligands
GOL
Metals
_BR ×4
Waters ×231
* Residue conservation analysis
PDB id:
2x40
Name: Hydrolase
Title: Structure of beta-glucosidase 3b from thermotoga neapolitana in complex with glycerol
Structure: Beta-glucosidase. Chain: a. Synonym: beta-glucosidase 3b. Engineered: yes
Source: Thermotoga neapolitana. Organism_taxid: 309803. Strain: dsm 4359. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: german collection of microorganisms (dsm)
Resolution:
2.31Å     R-factor:   0.176     R-free:   0.232
Authors: T.Pozzo,E.N.Karlsson,D.T.Logan
Key ref: T.Pozzo et al. (2010). Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3. J Mol Biol, 397, 724-739. PubMed id: 20138890 DOI: 10.1016/j.jmb.2010.01.072
Date:
28-Jan-10     Release date:   09-Feb-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q0GC07  (Q0GC07_THENN) -  Beta-glucosidase
Seq:
Struc:
 
Seq:
Struc:
721 a.a.
713 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.21  - Beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/j.jmb.2010.01.072 J Mol Biol 397:724-739 (2010)
PubMed id: 20138890  
 
 
Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3.
T.Pozzo, J.L.Pasten, E.N.Karlsson, D.T.Logan.
 
  ABSTRACT  
 
Based on sequence and phylogenetic analyses, glycoside hydrolase (GH) family 3 can be divided into several clusters that differ in the length of their primary sequences. However, structural data on representatives of GH3 are still scarce, since only three of their structures are known and only one of them has been thoroughly characterized-that of an exohydrolase from barley. To allow a deeper structural understanding of the GH3 family, we have determined the crystal structure of the thermostable beta-glucosidase from Thermotoga neapolitana, which has potentially important applications in environmentally friendly industrial biosynthesis at a resolution of 2.05 A. Selected active-site mutants have been characterized kinetically, and the structure of the mutant D242A is presented at 2.1 A resolution. Bgl3B from Th. neapolitana is the first example of a GH3 glucosidase with a three-domain structure. It is composed of an (alpha/beta)(8) domain similar to a triose phosphate isomerase barrel, a five-stranded alpha/beta sandwich domain (both of which are important for active-site organization), and a C-terminal fibronectin type III domain of unknown function. Remarkably, the direction of the second beta-strand of the triose phosphate isomerase barrel domain is reversed, which has implications for the active-site shape. The active site, at the interface of domains 1 and 2, is much more open to solvent than the corresponding site in the structurally homologous enzyme from barley, and only the -1 site is well defined. The structures, in combination with kinetic studies of active-site variants, allow the identification of essential catalytic residues (the nucleophile D242 and the acid/base E458), as well as other residues at the -1 subsite, including D58 and W243, which, by mutagenesis, are shown to be important for substrate accommodation/interaction. The position of the fibronectin type III domain excludes a direct participation of this domain in the recognition of small substrates, although it may be involved in the anchoring of the enzyme on large polymeric substrates and in thermostability.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20821204 J.Marín-Navarro, L.Gurgu, S.Alamar, and J.Polaina (2011).
Structural and functional analysis of hybrid enzymes generated by domain shuffling between Saccharomyces cerevisiae (var. diastaticus) Sta1 glucoamylase and Saccharomycopsis fibuligera Bgl1 β-glucosidase.
  Appl Microbiol Biotechnol, 89, 121-130.  
20376631 C.S.Park, M.H.Yoo, K.H.Noh, and D.K.Oh (2010).
Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.
  Appl Microbiol Biotechnol, 87, 9.  
20662765 E.Yoshida, M.Hidaka, S.Fushinobu, T.Koyanagi, H.Minami, H.Tamaki, M.Kitaoka, T.Katayama, and H.Kumagai (2010).
Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus.
  Biochem J, 431, 39-49.
PDB codes: 3abz 3ac0
21221939 H.W.Ji, and C.J.Cha (2010).
Identification and functional analysis of a gene encoding β-glucosidase from the brown-rot basidiomycete Fomitopsis palustris.
  J Microbiol, 48, 808-813.  
20717535 S.Luang, J.R.Ketudat Cairns, V.A.Streltsov, and M.Hrmova (2010).
Crystallisation of Wild-Type and Variant Forms of a Recombinant Plant Enzyme beta-d-Glucan Glucohydrolase from Barley (Hordeum vulgare L.) and Preliminary X-ray Analysis.
  Int J Mol Sci, 11, 2759-2769.  
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.