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PDBsum entry 1bga

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protein Protein-protein interface(s) links
Glycosidase PDB id
1bga
Jmol
Contents
Protein chains
447 a.a. *
Waters ×1541
* Residue conservation analysis
PDB id:
1bga
Name: Glycosidase
Title: Beta-glucosidase a from bacillus polymyxa
Structure: Beta-glucosidase a. Chain: a, b, c, d. Synonym: bga. Engineered: yes
Source: Paenibacillus polymyxa. Organism_taxid: 1406. Atcc: 842. Gene: bgla. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
2.40Å     R-factor:   0.200     R-free:   0.270
Authors: J.Sanz-Aparicio,J.A.Hermoso,M.Martinez-Ripoll,J.Polaina
Key ref:
J.Sanz-Aparicio et al. (1998). Crystal structure of beta-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases. J Mol Biol, 275, 491-502. PubMed id: 9466926 DOI: 10.1006/jmbi.1997.1467
Date:
04-Apr-97     Release date:   15-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22073  (BGLA_PAEPO) -  Beta-glucosidase A
Seq:
Struc:
448 a.a.
447 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   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1006/jmbi.1997.1467 J Mol Biol 275:491-502 (1998)
PubMed id: 9466926  
 
 
Crystal structure of beta-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases.
J.Sanz-Aparicio, J.A.Hermoso, M.Martínez-Ripoll, J.L.Lequerica, J.Polaina.
 
  ABSTRACT  
 
Family 1 glycosyl hydrolases are a very relevant group of enzymes because of the diversity of biological roles in which they are involved, and their generalized occurrence in all sorts of living organisms. The biological plasticity of these enzymes is a consequence of the variety of beta-glycosidic substrates that they can hydrolyze: disaccharides such as cellobiose and lactose, phosphorylated disaccharides, cyanogenic glycosides, etc. The crystal structure of BglA, a member of the family, has been determined in the native state and complexed with gluconate ligand, at 2.4 A and 2.3 A resolution, respectively. The subunits of the octameric enzyme display the (alpha/beta)8 barrel structural fold previously reported for other family 1 enzymes. However, significant structural differences have been encountered in the loops surrounding the active-center cavity. These differences make a wide and extended cavity in BglA, which seems to be able to accommodate substrates longer than cellobiose, its natural substrate. Furthermore, a third sub-site is encountered, which might have some connection with the transglycosylating activity associated to this enzyme and its certain activity against beta-1,4 oligosaccharides composed of more than two units of glucose. The particular geometry of the cavity which contains the active center of BglA must therefore account for both, hydrolytic and transglycosylating activities. A potent and well known inhibitor of different glycosidases, D-glucono-1,5-lactone, was used in an attempt to define interactions of the substrate with specific protein residues. Although the lactone has transformed into gluconate under crystallizing conditions, the open species still binds the enzyme, the conformation of its chain mimicking the true inhibitor. From the analysis of the enzyme-ligand hydrogen bonding interactions, a detailed picture of the active center can be drawn, for a family 1 enzyme. In this way, Gln20, His121, Tyr296, Glu405 and Trp406 are identified as determinant residues in the recognition of the substrate. In particular, two bidentate hydrogen bonds made by Gln20 and Glu405, could conform the structural explanation for the ability of most members of the family for displaying both, glucosidase and galactosidase activity.
 
  Selected figure(s)  
 
Figure 1.
Figure 6.
Figure 6. Electron density in the enzyme-gluconate complex. A stereo-view of the active site with the final model for the ligand superimposed into the (2F[o] − F[c]) contoured at 0.9σ.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 275, 491-502) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21046402 H.Xu, A.S.Xiong, W.Zhao, Y.S.Tian, R.H.Peng, J.M.Chen, and Q.H.Yao (2011).
Characterization of a Glucose-, Xylose-, Sucrose-, and D: -Galactose-Stimulated β-Glucosidase from the Alkalophilic Bacterium Bacillus halodurans C-125.
  Curr Microbiol, 62, 833-839.  
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
β-Glucosidases.
  Cell Mol Life Sci, 67, 3389-3405.  
19955176 M.Behrendt, J.Polaina, and H.Y.Naim (2010).
Structural hierarchy of regulatory elements in the folding and transport of an intestinal multidomain protein.
  J Biol Chem, 285, 4143-4152.  
19388085 W.Liu, J.Hong, D.R.Bevan, and Y.H.Zhang (2009).
Fast identification of thermostable beta-glucosidase mutants on cellobiose by a novel combinatorial selection/screening approach.
  Biotechnol Bioeng, 103, 1087-1094.  
18712828 K.H.Nam, S.J.Kim, M.Y.Kim, J.H.Kim, Y.S.Yeo, C.M.Lee, H.K.Jun, and K.Y.Hwang (2008).
Crystal structure of engineered beta-glucosidase from a soil metagenome.
  Proteins, 73, 788-793.
PDB code: 3cmj
18759236 K.M.Cho, S.J.Hong, R.K.Math, S.M.Islam, J.O.Kim, Y.H.Lee, H.Kim, and H.D.Yun (2008).
Cloning of two cellulase genes from endophytic Paenibacillus polymyxa GS01 and comparison with cel 44C-man 26A.
  J Basic Microbiol, 48, 464-472.  
18378601 L.G.Ljungdahl (2008).
The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.
  Ann N Y Acad Sci, 1125, 308-321.  
18422657 L.M.Mendonça, and S.R.Marana (2008).
The role in the substrate specificity and catalysis of residues forming the substrate aglycone-binding site of a beta-glycosidase.
  FEBS J, 275, 2536-2547.  
18023045 T.Tsukada, K.Igarashi, S.Fushinobu, and M.Samejima (2008).
Role of subsite +1 residues in pH dependence and catalytic activity of the glycoside hydrolase family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium.
  Biotechnol Bioeng, 99, 1295-1302.  
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
18033585 J.Stöckigt, and S.Panjikar (2007).
Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis.
  Nat Prod Rep, 24, 1382-1400.  
17238236 M.Ferrer, A.Beloqui, O.V.Golyshina, F.J.Plou, A.Neef, T.N.Chernikova, L.Fernández-Arrojo, I.Ghazi, A.Ballesteros, K.Elborough, K.N.Timmis, and P.N.Golyshin (2007).
Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome.
  Biotechnol J, 2, 207-213.  
17503162 M.León, P.Isorna, M.Menéndez, J.Sanz-Aparicio, and J.Polaina (2007).
Comparative study and mutational analysis of distinctive structural elements of hyperthermophilic enzymes.
  Protein J, 26, 435-444.
PDB code: 1uwi
16172888 H.Bach, and D.L.Gutnick (2006).
Novel polysaccharide-protein-based amphipathic formulations.
  Appl Microbiol Biotechnol, 71, 34-38.  
16912849 K.M.Cho, S.Y.Hong, S.M.Lee, Y.H.Kim, G.G.Kahng, H.Kim, and H.D.Yun (2006).
A cel44C-man26A gene of endophytic Paenibacillus polymyxa GS01 has multi-glycosyl hydrolases in two catalytic domains.
  Appl Microbiol Biotechnol, 73, 618-630.  
  16880561 W.Chuenchor, S.Pengthaisong, J.Yuvaniyama, R.Opassiri, J.Svasti, and J.R.Ketudat Cairns (2006).
Purification, crystallization and preliminary X-ray analysis of rice BGlu1 beta-glucosidase with and without 2-deoxy-2-fluoro-beta-D-glucoside.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 798-801.  
16205911 K.M.Harada, K.Tanaka, Y.Fukuda, W.Hashimoto, and K.Murata (2005).
Degradation of rice bran hemicellulose by Paenibacillus sp. strain HC1: gene cloning, characterization and function of beta-D-glucosidase as an enzyme involved in degradation.
  Arch Microbiol, 184, 215-224.  
15846595 S.M.Hancock, K.Corbett, A.P.Fordham-Skelton, J.A.Gatehouse, and B.G.Davis (2005).
Developing promiscuous glycosidases for glycoside synthesis: residues W433 and E432 in Sulfolobus solfataricus beta-glycosidase are important glucoside- and galactoside-specificity determinants.
  Chembiochem, 6, 866-875.  
16269771 S.Timmusk, N.Grantcharova, and E.G.Wagner (2005).
Paenibacillus polymyxa invades plant roots and forms biofilms.
  Appl Environ Microbiol, 71, 7292-7300.  
16082555 T.H.Park, K.W.Choi, C.S.Park, S.B.Lee, H.Y.Kang, K.J.Shon, J.S.Park, and J.Cha (2005).
Substrate specificity and transglycosylation catalyzed by a thermostable beta-glucosidase from marine hyperthermophile Thermotoga neapolitana.
  Appl Microbiol Biotechnol, 69, 411-422.  
14660638 J.K.McCarthy, A.Uzelac, D.F.Davis, and D.E.Eveleigh (2004).
Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution.
  J Biol Chem, 279, 11495-11502.  
15148317 L.Verdoucq, J.Morinière, D.R.Bevan, A.Esen, A.Vasella, B.Henrissat, and M.Czjze (2004).
Structural determinants of substrate specificity in family 1 beta-glucosidases: novel insights from the crystal structure of sorghum dhurrinase-1, a plant beta-glucosidase with strict specificity, in complex with its natural substrate.
  J Biol Chem, 279, 31796-31803.
PDB codes: 1v02 1v03 1v08
15340929 T.Akiba, M.Nishio, I.Matsui, and K.Harata (2004).
X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii.
  Proteins, 57, 422-431.
PDB code: 1vff
15252054 Y.W.Kim, S.S.Lee, R.A.Warren, and S.G.Withers (2004).
Directed evolution of a glycosynthase from Agrobacterium sp. increases its catalytic activity dramatically and expands its substrate repertoire.
  J Biol Chem, 279, 42787-42793.  
12596260 E.Bismuto, F.Febbraio, S.Limongelli, R.Briante, and R.Nucci (2003).
Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability.
  Proteins, 51, 10-20.  
12684498 L.Verdoucq, M.Czjzek, J.Moriniere, D.R.Bevan, and A.Esen (2003).
Mutational and structural analysis of aglycone specificity in maize and sorghum beta-glucosidases.
  J Biol Chem, 278, 25055-25062.
PDB code: 1h49
14653813 S.R.Marana, L.M.Mendonça, E.H.Andrade, W.R.Terra, and C.Ferreira (2003).
The role of residues R97 and Y331 in modulating the pH optimum of an insect beta-glycosidase of family 1.
  Eur J Biochem, 270, 4866-4875.  
12837801 X.Wang, X.He, S.Yang, X.An, W.Chang, and D.Liang (2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
  J Bacteriol, 185, 4248-4255.
PDB code: 1np2
12012341 B.Cobucci-Ponzano, M.Moracci, B.Di Lauro, M.Ciaramella, R.D'Avino, and M.Rossi (2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
  Proteins, 48, 98.  
11784319 J.G.Berrin, W.R.McLauchlan, P.Needs, G.Williamson, A.Puigserver, P.A.Kroon, and N.Juge (2002).
Functional expression of human liver cytosolic beta-glucosidase in Pichia pastoris. Insights into its role in the metabolism of dietary glucosides.
  Eur J Biochem, 269, 249-258.  
12200312 M.Saloheimo, J.Kuja-Panula, E.Ylösmäki, M.Ward, and M.Penttilä (2002).
Enzymatic properties and intracellular localization of the novel Trichoderma reesei beta-glucosidase BGLII (cel1A).
  Appl Environ Microbiol, 68, 4546-4553.  
12153567 S.R.Marana, W.R.Terra, and C.Ferreira (2002).
The role of amino-acid residues Q39 and E451 in the determination of substrate specificity of the Spodoptera frugiperda beta-glycosidase.
  Eur J Biochem, 269, 3705-3714.  
11900558 T.Kaper, H.H.van Heusden, B.van Loo, A.Vasella, J.van der Oost, and W.M.de Vos (2002).
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
  Biochemistry, 41, 4147-4155.  
12487426 Y.Bhatia, S.Mishra, and V.S.Bisaria (2002).
Microbial beta-glucosidases: cloning, properties, and applications.
  Crit Rev Biotechnol, 22, 375-407.  
11134937 J.Vévodová, J.Marek, J.Zouhar, B.Brzobohatý, and X.D.Su (2001).
Purification, crystallization and preliminary X-ray analysis of a maize cytokinin glucoside specific beta-glucosidase.
  Acta Crystallogr D Biol Crystallogr, 57, 140-142.  
11342030 S.R.Marana, M.Jacobs-Lorena, W.R.Terra, and C.Ferreira (2001).
Amino acid residues involved in substrate binding and catalysis in an insect digestive beta-glycosidase.
  Biochim Biophys Acta, 1545, 41-52.  
11679733 X.Y.He, X.Q.Wang, S.J.Yang, W.R.Chang, and D.C.Liang (2001).
Overexpression, purification, crystallization and preliminary crystallographic studies on a thermostable beta-glycosidase from Thermus nonproteolyticus HG102.
  Acta Crystallogr D Biol Crystallogr, 57, 1650-1651.  
10788490 G.Gonzalez-Blasco, J.Sanz-Aparicio, B.Gonzalez, J.A.Hermoso, and J.Polaina (2000).
Directed evolution of beta -glucosidase A from Paenibacillus polymyxa to thermal resistance.
  J Biol Chem, 275, 13708-13712.  
10736164 J.H.Lebbink, T.Kaper, P.Bron, J.van der Oost, and W.M.de Vos (2000).
Improving low-temperature catalysis in the hyperthermostable Pyrococcus furiosus beta-glucosidase CelB by directed evolution.
  Biochemistry, 39, 3656-3665.  
11106394 M.Czjzek, M.Cicek, V.Zamboni, D.R.Bevan, B.Henrissat, and A.Esen (2000).
The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
  Proc Natl Acad Sci U S A, 97, 13555-13560.
PDB codes: 1e4l 1e4n 1e55 1e56
10819960 T.Kaper, J.H.Lebbink, J.Pouwels, J.Kopp, G.E.Schulz, J.van der Oost, and W.M.de Vos (2000).
Comparative structural analysis and substrate specificity engineering of the hyperthermostable beta-glucosidase CelB from Pyrococcus furiosus.
  Biochemistry, 39, 4963-4970.  
  10583980 A.C.Adam, G.González-Blasco, M.Rubio-Texeira, and J.Polaina (1999).
Transformation of Escherichia coli with DNA from Saccharomyces cerevisiae cell lysates.
  Appl Environ Microbiol, 65, 5303-5306.  
10089468 A.Guasch, M.Vallmitjana, R.Pérez, E.Querol, J.A.Pérez-Pons, and M.Coll (1999).
Cloning, overexpression, crystallization and preliminary X-ray analysis of a family 1 beta--glucosidase from Streptomyces.
  Acta Crystallogr D Biol Crystallogr, 55, 679-682.  
9849940 J.Sanz-Aparicio, J.A.Hermoso, M.Martínez-Ripoll, B.González, C.López-Camacho, and J.Polaina (1998).
Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of beta-glucosidase A from Bacillus polymyxa.
  Proteins, 33, 567-576.
PDB code: 1e4i
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 code is shown on the right.