6GYA

Amylase in complex with branched ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report



Literature

The structure of the AliC GH13 alpha-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the alpha-amylase family.

Agirre, J.Moroz, O.Meier, S.Brask, J.Munch, A.Hoff, T.Andersen, C.Wilson, K.S.Davies, G.J.

(2019) Acta Crystallogr D Struct Biol 75: 1-7

  • DOI: 10.1107/S2059798318014900
  • Primary Citation of Related Structures:  
    6GYA, 6GXV

  • PubMed Abstract: 
  • α-Amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The degradation of starch is rendered difficult by the presence of varying degrees of α-1,6 branch points and their possible accommodation within the active ...

    α-Amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The degradation of starch is rendered difficult by the presence of varying degrees of α-1,6 branch points and their possible accommodation within the active centre of α-amylase enzymes. Given the myriad industrial uses for starch and thus also for α-amylase-catalysed starch degradation and modification, there is considerable interest in how different α-amylases might accommodate these branches, thus impacting on the potential processing of highly branched post-hydrolysis remnants (known as limit dextrins) and societal applications. Here, it was sought to probe the branch-point accommodation of the Alicyclobacillus sp. CAZy family GH13 α-amylase AliC, prompted by the observation of a molecule of glucose in a position that may represent a branch point in an acarbose complex solved at 2.1 Å resolution. Limit digest analysis by two-dimensional NMR using both pullulan (a regular linear polysaccharide of α-1,4, α-1,4, α-1,6 repeating trisaccharides) and amylopectin starch showed how the Alicyclobacillus sp. enzyme could accept α-1,6 branches in at least the -2, +1 and +2 subsites, consistent with the three-dimensional structures with glucosyl moieties in the +1 and +2 subsites and the solvent-exposure of the -2 subsite 6-hydroxyl group. Together, the work provides a rare insight into branch-point acceptance in these industrial catalysts.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
A-amylaseA, B, C, D484Alicyclobacillus sp.Mutation(s): 0 
Find proteins for A0A3P8MUS3 (Alicyclobacillus sp)
Explore A0A3P8MUS3 
Go to UniProtKB:  A0A3P8MUS3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E, G, I, K
3 N/A
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
F, H, J, L
2 N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download CCD File 
A, B, C
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
BGC
Query on BGC

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B, C, D
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.18α = 90
b = 212.18β = 90
c = 172.22γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
BUCCANEERmodel building
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-05-29
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-08-21
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary