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PDBsum entry 1bag

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protein ligands metals links
Alpha-amylase PDB id
1bag
Jmol
Contents
Protein chain
425 a.a. *
Ligands
GLC-GLC-GLC-GLC-
BGC
Metals
_CA ×3
Waters ×146
* Residue conservation analysis
PDB id:
1bag
Name: Alpha-amylase
Title: Alpha-amylase from bacillus subtilis complexed with maltopentaose
Structure: Alpha-1,4-glucan-4-glucanohydrolase. Chain: a. Synonym: alpha-amylase. Engineered: yes. Mutation: yes. Other_details: complexed with maltopentaose
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: amy. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
2.50Å     R-factor:   0.198     R-free:   0.252
Authors: Z.Fujimoto,H.Mizuno,K.Takase,N.Doui
Key ref:
Z.Fujimoto et al. (1998). Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose. J Mol Biol, 277, 393-407. PubMed id: 9514750 DOI: 10.1006/jmbi.1997.1599
Date:
30-Jan-98     Release date:   21-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00691  (AMY_BACSU) -  Alpha-amylase
Seq:
Struc:
 
Seq:
Struc:
659 a.a.
425 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.1  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1006/jmbi.1997.1599 J Mol Biol 277:393-407 (1998)
PubMed id: 9514750  
 
 
Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.
Z.Fujimoto, K.Takase, N.Doui, M.Momma, T.Matsumoto, H.Mizuno.
 
  ABSTRACT  
 
The X-ray crystal structure of a catalytic-site mutant EQ208 [Glu208-->Gln] of alpha-amylase from Bacillus subtilis cocrystallized with maltopentaose (G5) and acarbose has been determined by multiple isomorphous replacement at 2.5 A resolution. Restrained crystallographic refinement has resulted in an R-factor of 19.8% in the 7.0 to 2.5 A resolution range. EQ208 consists of three domains containing a (beta/alpha)8-barrel as observed in other alpha-amylases. Clear connected density corresponding to a pentasaccharide was observed, which was considered as the G5 molecule based on the high affinity of EQ208 for G5 that could replace pre-bound acarbose or a possible transglycosylation product of acarbose. The conformation around the third alpha-(1,4)-glucosidic bond makes a sharp turn, allowing the substrate to fit into the L-shaped cleft. Aromatic residues build the walls of the substrate binding cleft and leucine residues form the inner curvature of the cleft. The amide nitrogen of Gln208 forms a hydrogen bond with the glucosidic oxygen in the scissile bond between Glc3 and Glc4 (Glc1 is the non-reducing end glucose residue of the substrate). This hydrogen-bonding manner may correspond to that of the protonated state of Glu208 in the initial kinetic complex between wild-type enzyme and substrate. The amide oxygen of Gln208 is anchored by two hydrogen bonds with Ala177 and a water molecule, assisting to make the amide proton point precisely to the place of the catalytic attack. The carboxyl oxygen atoms of the other catalytic-site residues Asp176 and Asp269 form hydrogen bonds with the oxygen atoms of Glc3. The carboxyl group of Asp176 has non-bonded contacts to the anomeric carbon atom and to the endocyclic oxygen atom of Glc3. These results suggest that Glu208 acts as a general acid and Asp176 as a general base. Glc3 forms seven hydrogen bonds with the surrounding protein groups and a stacking interaction with Tyr62, which is consistent with the fact that Glc3 has the lowest mean thermal factor of 13.2 A2 among the five sugar residues. Three calcium ions are found, one of which is positioned near the substrate binding site as found in other alpha-amylases and could contribute to stabilization of the structure of the active site.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereoview of the G5-binding structure of EQ208. Residues involved in the hydrophilic interaction are colored by elements and those in the hydrophobic interaction are shown in orange.
Figure 6.
Figure 6. Schematic drawing of the hydrogen-bonding network between EQ208 and G5. Two water molecules mediating hydrogen bonds and hydrophobic residues interacting with G5 are also indicated.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 393-407) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19626353 M.S.Till, and G.M.Ullmann (2010).
McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm.
  J Mol Model, 16, 419-429.  
19880384 Y.Y.Tseng, Z.J.Chen, and W.H.Li (2010).
fPOP: footprinting functional pockets of proteins by comparative spatial patterns.
  Nucleic Acids Res, 38, D288-D295.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
18552192 J.Y.Damián-Almazo, A.Moreno, A.López-Munguía, X.Soberón, F.González-Muñoz, and G.Saab-Rincón (2008).
Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.
  Appl Environ Microbiol, 74, 5168-5177.  
17516156 F.Khodagholi, B.Eftekharzadeh, and R.Yazdanparast (2007).
Comparative evaluation of alpha-amylase refolding through two different artificial chaperone systems.
  Protein J, 26, 293-301.  
17294116 Y.Y.Tseng, and J.Liang (2007).
Predicting enzyme functional surfaces and locating key residues automatically from structures.
  Ann Biomed Eng, 35, 1037-1042.  
16551661 F.Pazos, A.Rausell, and A.Valencia (2006).
Phylogeny-independent detection of functional residues.
  Bioinformatics, 22, 1440-1448.  
16391027 K.Kurosawa, T.Hosaka, N.Tamehiro, T.Inaoka, and K.Ochi (2006).
Improvement of alpha-amylase production by modulation of ribosomal component protein S12 in Bacillus subtilis 168.
  Appl Environ Microbiol, 72, 71-77.  
15722449 R.Maurus, A.Begum, H.H.Kuo, A.Racaza, S.Numao, C.Andersen, J.W.Tams, J.Vind, C.M.Overall, S.G.Withers, and G.D.Brayer (2005).
Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase.
  Protein Sci, 14, 743-755.
PDB codes: 1xgz 1xh0 1xh1 1xh2
15599521 S.Kang, C.Vieille, and J.G.Zeikus (2005).
Identification of Pyrococcus furiosus amylopullulanase catalytic residues.
  Appl Microbiol Biotechnol, 66, 408-413.  
16030022 X.Robert, R.Haser, H.Mori, B.Svensson, and N.Aghajari (2005).
Oligosaccharide binding to barley alpha-amylase 1.
  J Biol Chem, 280, 32968-32978.
PDB codes: 1rp8 1rp9 1rpk
15356864 G.André, and V.Tran (2004).
Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.
  Biopolymers, 75, 95.  
14660599 K.S.Bak-Jensen, G.André, T.E.Gottschalk, G.Paës, V.Tran, and B.Svensson (2004).
Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1.
  J Biol Chem, 279, 10093-10102.  
15046926 L.Tuovinen, S.Peltonen, M.Liikola, M.Hotakainen, M.Lahtela-Kakkonen, A.Poso, and K.Järvinen (2004).
Drug release from starch-acetate microparticles and films with and without incorporated alpha-amylase.
  Biomaterials, 25, 4355-4362.  
12752453 H.B.Fritzsche, T.Schwede, and G.E.Schulz (2003).
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92.
  Eur J Biochem, 270, 2332-2341.
PDB code: 1h3g
14517232 K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, and D.Schomburg (2003).
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
  EMBO J, 22, 4922-4932.
PDB codes: 1pz2 1pz3 1qw8 1qw9
14617662 M.Kagawa, Z.Fujimoto, M.Momma, K.Takase, and H.Mizuno (2003).
Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.
  J Bacteriol, 185, 6981-6984.
PDB code: 1ua7
14511369 N.Oudjeriouat, Y.Moreau, M.Santimone, B.Svensson, G.Marchis-Mouren, and V.Desseaux (2003).
On the mechanism of alpha-amylase.
  Eur J Biochem, 270, 3871-3879.  
12581203 S.Janecek, B.Svensson, and E.A.MacGregor (2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
  Eur J Biochem, 270, 635-645.  
12906828 X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, and N.Aghajari (2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
  Structure, 11, 973-984.
PDB codes: 1ht6 1p6w
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
11257505 E.A.MacGregor, S.Janecek, and B.Svensson (2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
  Biochim Biophys Acta, 1546, 1.  
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.  
11717490 M.Akita, A.Suzuki, T.Kobayashi, S.Ito, and T.Yamane (2001).
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
  Acta Crystallogr D Biol Crystallogr, 57, 1786-1792.
PDB code: 1ee6
11257602 T.Hansson, T.Kaper, J.van Der Oost, W.M.de Vos, and P.Adlercreutz (2001).
Improved oligosaccharide synthesis by protein engineering of beta-glucosidase CelB from hyperthermophilic Pyrococcus furiosus.
  Biotechnol Bioeng, 73, 203-210.  
10666605 D.Suvd, K.Takase, Z.Fujimoto, M.Matsumura, and H.Mizuno (2000).
Purification, crystallization and preliminary X-ray crystallographic study of alpha-amylase from Bacillus stearothermophilus.
  Acta Crystallogr D Biol Crystallogr, 56, 200-202.  
  11082203 I.Przylas, Y.Terada, K.Fujii, T.Takaha, W.Saenger, and N.Sträter (2000).
X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans.
  Eur J Biochem, 267, 6903-6913.
PDB code: 1esw
10877806 K.Ohdan, T.Kuriki, H.Takata, H.Kaneko, and S.Okada (2000).
Introduction of raw starch-binding domains into Bacillus subtilis alpha-amylase by fusion with the starch-binding domain of Bacillus cyclomaltodextrin glucanotransferase.
  Appl Environ Microbiol, 66, 3058-3064.  
10473583 J.S.Kim, S.S.Cha, H.J.Kim, T.J.Kim, N.C.Ha, S.T.Oh, H.S.Cho, M.J.Cho, M.J.Kim, H.S.Lee, J.W.Kim, K.Y.Choi, K.H.Park, and B.H.Oh (1999).
Crystal structure of a maltogenic amylase provides insights into a catalytic versatility.
  J Biol Chem, 274, 26279-26286.
PDB code: 1sma
10469642 K.A.Watson, C.McCleverty, S.Geremia, S.Cottaz, H.Driguez, and L.N.Johnson (1999).
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question.
  EMBO J, 18, 4619-4632.
PDB codes: 1e4o 1qm5
  10508102 K.Ohdan, T.Kuriki, H.Kaneko, J.Shimada, T.Takada, Z.Fujimoto, H.Mizuno, and S.Okada (1999).
Characteristics of two forms of alpha-amylases and structural implication.
  Appl Environ Microbiol, 65, 4652-4658.  
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.