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PDBsum entry 1uok

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protein links
Glucosidase PDB id
1uok
Jmol
Contents
Protein chain
558 a.a. *
Waters ×221
* Residue conservation analysis
PDB id:
1uok
Name: Glucosidase
Title: Crystal structure of b. Cereus oligo-1,6-glucosidase
Structure: Oligo-1,6-glucosidase. Chain: a. Engineered: yes
Source: Bacillus cereus. Organism_taxid: 1396. Atcc: atcc 7064. Collection: atcc 7064. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.192     R-free:   0.246
Authors: K.Watanabe,Y.Hata,H.Kizaki,Y.Katsube,Y.Suzuki
Key ref:
K.Watanabe et al. (1997). The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 A resolution: structural characterization of proline-substitution sites for protein thermostabilization. J Mol Biol, 269, 142-153. PubMed id: 9193006 DOI: 10.1006/jmbi.1997.1018
Date:
28-Jul-98     Release date:   16-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21332  (O16G_BACCE) -  Oligo-1,6-glucosidase
Seq:
Struc:
 
Seq:
Struc:
558 a.a.
558 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.10  - Oligo-1,6-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,6-alpha-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by alpha-amylase, and in isomaltose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1006/jmbi.1997.1018 J Mol Biol 269:142-153 (1997)
PubMed id: 9193006  
 
 
The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 A resolution: structural characterization of proline-substitution sites for protein thermostabilization.
K.Watanabe, Y.Hata, H.Kizaki, Y.Katsube, Y.Suzuki.
 
  ABSTRACT  
 
The crystal structure of oligo-1,6-glucosidase (dextrin 6-alpha-glucanohydrolase, EC 3.2.1.10) from Bacillus cereus ATCC7064 has been refined to 2.0 A resolution with an R-factor of 19.6% for 43,328 reflections. The final model contains 4646 protein atoms and 221 ordered water molecules with respective root-mean-square deviations of 0.015 A for bond lengths and of 3.166 degrees for bond angles from the ideal values. The structure consists of three domains: the N-terminal domain (residues 1 to 104 and 175 to 480), the subdomain (residues 105 to 174) and the C-terminal domain (residues 481 to 558). The N-terminal domain takes a (beta/alpha)8-barrel structure with additions of an alpha-helix (N alpha6') between the sixth strand Nbeta6 and the sixth helix N alpha6, an alpha-helix (N alpha7') between the seventh strand Nbeta7 and the seventh helix N alpha7 and three alpha-helices (N alpha8', N alpha8" and N alpha8'" between the eighth strand Nbeta8 and the eighth helix N alpha8. The subdomain is composed of an alpha-helix, a three-stranded antiparallel beta-sheet, and long intervening loops. The C-terminal domain has a beta-barrel structure of eight antiparallel beta-strands folded in double Greek key motifs, which is distorted in the sixth strand Cbeta6. Three catalytic residues, Asp199, Glu255 and Asp329, are located at the bottom of a deep cleft formed by the subdomain and a cluster of the two additional alpha-helices N alpha8' and N alpha8" in the (beta/alpha)8-barrel. The refined structure reveals the locations of 21 proline-substitution sites that are expected to be critical to protein thermostabilization from a sequence comparison among three Bacillus oligo-1,6-glucosidases with different thermostability. These sites lie in loops, beta-turns and alpha-helices, in order of frequency, except for Cys515 in the fourth beta-strand Cbeta4 of the C-terminal domain. The residues in beta-turns (Lys121, Glu208, Pro257, Glu290, Pro443, Lys457 and Glu487) are all found at their second positions, and those in alpha-helices (Asn109, Glu175, Thr261 and Ile403) are present at their N1 positions of the first helical turns. Those residues in both secondary structures adopt phi and phi values favorable for proline substitution. Residues preceding the 21 sites are mostly conserved upon proline occurrence at these 21 sites in more thermostable Bacillus oligo-1,6-glucosidases. These structural features with respect to the 21 sites indicate that the sites in beta-turns and alpha-helices have more essential prerequisites for proline substitution to thermostabilize the protein than those in loops. This well supports the previous finding that the replacement at the appropriate positions in beta-turns or alpha-helices is the most effective for protein thermostabilization by proline substitution.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Representations of B. cereus oligo-1,6-glucosidase: (a) the view perpendicular to the axis of the (b/a)8-barrel; (b) the view along the axis of the (b/a)8-barrel. a-Helices and b-strands of the N-terminal domain are colored yellow and red; one a-helix and three b-strands of the subdomain green and blue; and b-strands of the C-terminal domain purple, respectively. All drawings of the structure were made with the program MOLSCRIPT (Kraulis, 1991).
Figure 4.
Figure 4. Diagrams of the hydrogen bonding pattern among b-strands of (a) the N-terminal domain, (b) the subdomain, and (c) the C-terminal domain of B. cereus oligo-1,6-glucosidase.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 269, 142-153) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397496 S.Park, S.Hyun, and J.Yu (2011).
Selective α-glucosidase substrates and inhibitors containing short aromatic peptidyl moieties.
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20596542 A.Bhardwaj, S.Leelavathi, S.Mazumdar-Leighton, A.Ghosh, S.Ramakumar, and V.S.Reddy (2010).
The critical role of N- and C-terminal contact in protein stability and folding of a family 10 xylanase under extreme conditions.
  PLoS One, 5, e11347.  
20517292 J.Chillarón, M.Font-Llitjós, J.Fort, A.Zorzano, D.S.Goldfarb, V.Nunes, and M.Palacín (2010).
Pathophysiology and treatment of cystinuria.
  Nat Rev Nephrol, 6, 424-434.  
20812985 K.Yamamoto, H.Miyake, M.Kusunoki, and S.Osaki (2010).
Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.
  FEBS J, 277, 4205-4214.
PDB codes: 3a4a 3aj7
19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
  Appl Biochem Biotechnol, 160, 2401-2414.  
20487512 T.J.Taylor, and I.I.Vaisman (2010).
Discrimination of thermophilic and mesophilic proteins.
  BMC Struct Biol, 10, S5.  
20306186 X.Liang, Y.Bian, X.F.Tang, G.Xiao, and B.Tang (2010).
Enhancement of keratinolytic activity of a thermophilic subtilase by improving its autolysis resistance and thermostability under reducing conditions.
  Appl Microbiol Biotechnol, 87, 999.  
19418260 X.Q.Wu, J.Wang, Z.R.Lü, H.M.Tang, D.Park, S.H.Oh, J.Bhak, L.Shi, Y.D.Park, and F.Zou (2010).
Alpha-glucosidase folding during urea denaturation: enzyme kinetics and computational prediction.
  Appl Biochem Biotechnol, 160, 1341-1355.  
19074503 J.Arnórsdóttir, A.R.Sigtryggsdóttir, S.H.Thorbjarnardóttir, and M.M.Kristjánsson (2009).
Effect of proline substitutions on stability and kinetic properties of a cold adapted subtilase.
  J Biochem, 145, 325-329.  
18977771 K.Takano, R.Higashi, J.Okada, A.Mukaiyama, T.Tadokoro, Y.Koga, and S.Kanaya (2009).
Proline effect on the thermostability and slow unfolding of a hyperthermophilic protein.
  J Biochem, 145, 79-85.  
19830687 M.M.Islam, S.Sohya, K.Noguchi, S.Kidokoro, M.Yohda, and Y.Kuroda (2009).
Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations.
  Proteins, 77, 962-970.
PDB code: 2zvx
18552181 H.C.Lee, J.H.Kim, S.Y.Kim, and J.K.Lee (2008).
Isomaltose production by modification of the fructose-binding site on the basis of the predicted structure of sucrose isomerase from "Protaminobacter rubrum".
  Appl Environ Microbiol, 74, 5183-5194.  
17920282 H.Park, K.Y.Hwang, K.H.Oh, Y.H.Kim, J.Y.Lee, and K.Kim (2008).
Discovery of novel alpha-glucosidase inhibitors based on the virtual screening with the homology-modeled protein structure.
  Bioorg Med Chem, 16, 284-292.  
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
  18997332 K.Yamamoto, H.Miyake, M.Kusunoki, and S.Osaki (2008).
Crystallization and preliminary X-ray analysis of isomaltase from Saccharomyces cerevisiae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1024-1026.  
18049800 S.B.Mabrouk, E.B.Messaoud, D.Ayadi, S.Jemli, A.Roy, M.Mezghani, and S.Bejar (2008).
Cloning and sequencing of an original gene encoding a maltogenic amylase from Bacillus sp. US149 strain and characterization of the recombinant activity.
  Mol Biotechnol, 38, 211-219.  
18398906 T.Shirai, V.S.Hung, K.Morinaka, T.Kobayashi, and S.Ito (2008).
Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria.
  Proteins, 73, 126-133.
PDB code: 2ze0
17710363 X.X.Zhou, Y.B.Wang, Y.J.Pan, and W.F.Li (2008).
Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins.
  Amino Acids, 34, 25-33.  
17429573 G.Saelensminde, ..Halskau, R.Helland, N.P.Willassen, and I.Jonassen (2007).
Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins.
  Extremophiles, 11, 585-596.  
17430559 K.Mizuguchi, M.Sele, and M.V.Cubellis (2007).
Environment specific substitution tables for thermophilic proteins.
  BMC Bioinformatics, 8, S15.  
17617712 M.Nishimoto, H.Mori, T.Moteki, Y.Takamura, G.Iwai, Y.Miyaguchi, M.Okuyama, J.Wongchawalit, R.Surarit, J.Svasti, A.Kimura, and S.Chiba (2007).
Molecular cloning of cDNAs and genes for three alpha-glucosidases from European honeybees, Apis mellifera L., and heterologous production of recombinant enzymes in Pichia pastoris.
  Biosci Biotechnol Biochem, 71, 1703-1716.  
  17768352 W.Saburi, H.Hondoh, H.Unno, M.Okuyama, H.Mori, T.Nakada, Y.Matsuura, and A.Kimura (2007).
Crystallization and preliminary X-ray analysis of Streptococcus mutans dextran glucosidase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 774-776.  
17151473 J.Wongchawalit, T.Yamamoto, H.Nakai, Y.M.Kim, N.Sato, M.Nishimoto, M.Okuyama, H.Mori, O.Saji, C.Chanchao, S.Wongsiri, R.Surarit, J.Svasti, S.Chiba, and A.Kimura (2006).
Purification and characterization of alpha-glucosidase I from Japanese honeybee (Apis cerana japonica) and molecular cloning of its cDNA.
  Biosci Biotechnol Biochem, 70, 2889-2898.  
16247799 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, and N.Tanaka (2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
  Proteins, 61, 999.
PDB codes: 1vbr 1vbu
15746363 L.Wu, and R.G.Birch (2005).
Characterization of the highly efficient sucrose isomerase from Pantoea dispersa UQ68J and cloning of the sucrose isomerase gene.
  Appl Environ Microbiol, 71, 1581-1590.  
15012820 A.Murai, Y.Tsujimoto, H.Matsui, and K.Watanabe (2004).
An Aneurinibacillus sp. strain AM-1 produces a proline-specific aminopeptidase useful for collagen degradation.
  J Appl Microbiol, 96, 810-818.  
15291818 K.Yamamoto, A.Nakayama, Y.Yamamoto, and S.Tabata (2004).
Val216 decides the substrate specificity of alpha-glucosidase in Saccharomyces cerevisiae.
  Eur J Biochem, 271, 3414-3420.  
12819210 D.Zhang, N.Li, S.M.Lok, L.H.Zhang, and K.Swaminathan (2003).
Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism.
  J Biol Chem, 278, 35428-35434.
PDB code: 1m53
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
12323355 B.van den Burg, and V.G.Eijsink (2002).
Selection of mutations for increased protein stability.
  Curr Opin Biotechnol, 13, 333-337.  
12039719 D.Zhang, X.Li, and L.H.Zhang (2002).
Isomaltulose synthase from Klebsiella sp. strain LX3: gene cloning and characterization and engineering of thermostability.
  Appl Environ Microbiol, 68, 2676-2682.  
12423336 H.Mori, K.S.Bak-Jensen, and B.Svensson (2002).
Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
  Eur J Biochem, 269, 5377-5390.  
12364331 L.K.Skov, O.Mirza, D.Sprogøe, I.Dar, M.Remaud-Simeon, C.Albenne, P.Monsan, and M.Gajhede (2002).
Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity.
  J Biol Chem, 277, 47741-47747.
PDB codes: 1mvy 1mw0 1mw1 1mw2 1mw3
11856334 T.P.Frandsen, M.M.Palcic, and B.Svensson (2002).
Substrate recognition by three family 13 yeast alpha-glucosidases.
  Eur J Biochem, 269, 728-734.  
11737209 H.Mori, K.S.Bak-Jensen, T.E.Gottschalk, M.S.Motawia, I.Damager, B.L.Møller, and B.Svensson (2001).
Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6 of barley alpha-amylase 1.
  Eur J Biochem, 268, 6545-6558.  
11676021 K.Watanabe, K.Miyake, and Y.Suzuki (2001).
Identification of catalytic and substrate-binding site residues in Bacillus cereus ATCC7064 oligo-1,6-glucosidase.
  Biosci Biotechnol Biochem, 65, 2058-2064.  
10792537 L.Janda, J.Damborský, M.Petrícek, J.Spízek, and P.Tichý (2000).
Molecular characterization of the Thermomonospora curvata aglA gene encoding a thermotolerant alpha-1,4-glucosidase.
  J Appl Microbiol, 88, 773-783.  
10945254 S.Kashiwabara, S.Azuma, M.Tsuduki, and Y.Suzuki (2000).
The primary structure of the subunit in Bacillus thermoamyloliquefaciens KP1071 molecular weight 540,000 homohexameric alpha-glucosidase II belonging to the glycosyl hydrolase family 31.
  Biosci Biotechnol Biochem, 64, 1379-1393.  
9753433 K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, and C.Kratky (1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
  Biochemistry, 37, 13475-13485.
PDB code: 1yna
9862804 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
  Structure, 6, 1503-1516.
PDB code: 1b0i
  9836874 O.Bogin, M.Peretz, Y.Hacham, Y.Korkhin, F.Frolow, A.J.Kalb(Gilboa), and Y.Burstein (1998).
Enhanced thermal stability of Clostridium beijerinckii alcohol dehydrogenase after strategic substitution of amino acid residues with prolines from the homologous thermophilic Thermoanaerobacter brockii alcohol dehydrogenase.
  Protein Sci, 7, 1156-1163.  
9692189 S.Kashiwabara, Y.Matsuki, T.Kishimoto, and Y.Suzuki (1998).
Clustered proline residues around the active-site cleft in thermostable oligo-1,6-glucosidase of Bacillus flavocaldarius KP1228.
  Biosci Biotechnol Biochem, 62, 1093-1102.  
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.