Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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This is version 2.2 of the entry. See complete history


Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.

Fujimoto, Z.Takase, K.Doui, N.Momma, M.Matsumoto, T.Mizuno, H.

(1998) J Mol Biol 277: 393-407

  • DOI: https://doi.org/10.1006/jmbi.1997.1599
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, Ibaraki, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE425Bacillus subtilisMutation(s): 3 
Gene Names: AMY
Find proteins for P00691 (Bacillus subtilis (strain 168))
Explore P00691 
Go to UniProtKB:  P00691
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00691
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G43441FW
GlyCosmos:  G43441FW
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.59α = 90
b = 74.06β = 90
c = 117.01γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2024-02-07
    Changes: Data collection