1WPC

Crystal structure of maltohexaose-producing amylase complexed with pseudo-maltononaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



Literature

Biochemical and crystallographic analyses of maltohexaose-producing amylase from alkalophilic Bacillus sp. 707

Kanai, R.Haga, K.Akiba, T.Yamane, K.Harata, K.

(2004) Biochemistry 43: 14047-14056

  • DOI: 10.1021/bi048489m
  • Primary Citation of Related Structures:  
    1WPC, 1WP6

  • PubMed Abstract: 
  • Maltohexaose-producing amylase, called G6-amylase (EC 3.2.1.98), from alkalophilic Bacillus sp.707 predominantly produces maltohexaose (G6) from starch and related alpha-1,4-glucans. To elucidate the reaction mechanism of G6-amylase, the enzyme activ ...

    Maltohexaose-producing amylase, called G6-amylase (EC 3.2.1.98), from alkalophilic Bacillus sp.707 predominantly produces maltohexaose (G6) from starch and related alpha-1,4-glucans. To elucidate the reaction mechanism of G6-amylase, the enzyme activities were evaluated and crystal structures were determined for the native enzyme and its complex with pseudo-maltononaose at 2.1 and 1.9 A resolutions, respectively. The optimal condition for starch-degrading reaction activity was found at 45 degrees C and pH 8.8, and the enzyme produced G6 in a yield of more than 30% of the total products from short-chain amylose (DP = 17). The crystal structures revealed that Asp236 is a nucleophilic catalyst and Glu266 is a proton donor/acceptor. Pseudo-maltononaose occupies subsites -6 to +3 and induces the conformational change of Glu266 and Asp333 to form a salt linkage with the N-glycosidic amino group and a hydrogen bond with secondary hydroxyl groups of the cyclitol residue bound to subsite -1, respectively. The indole moiety of Trp140 is stacked on the cyclitol and 4-amino-6-deoxyglucose residues located at subsites -6 and -5 within a 4 A distance. Such a face-to-face short contact may regulate the disposition of the glucosyl residue at subsite -6 and would govern the product specificity for G6 production.


    Related Citations: 
    • Cloning of a gene for maltohexaose producing amylase of an alkalophilic Bacillus and hyper-production of the enzyme in Bacillus subtilis cells
      Kimura, K., Tsukamoto, A., Ishii, Y., Takano, T., Yamane, K.
      (1988) Appl Microbiol Biotechnol 27: 372

    Organizational Affiliation

    Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucan 1,4-alpha-maltohexaosidaseA485Bacillus sp. 707Mutation(s): 0 
EC: 3.2.1.98
Find proteins for P19571 (Bacillus sp. (strain 707))
Explore P19571 
Go to UniProtKB:  P19571
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
4 N/A
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose
C
3 N/A
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
D, E
2 N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACI
Query on ACI

Download CCD File 
A
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
D, Ealpha-maltoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.41α = 90
b = 82.49β = 90
c = 126.88γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary