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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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: https://doi.org/10.1107/S2059798318014900
  • Primary Citation of Related Structures:  
    6GXV, 6GYA

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A-amylase
A, B, C, D
484Alicyclobacillus sp.Mutation(s): 0 
UniProt
Find proteins for A0A3P8MUS3 (Alicyclobacillus sp)
Explore A0A3P8MUS3 
Go to UniProtKB:  A0A3P8MUS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3P8MUS3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E, G, I, K
3N/A
Glycosylation Resources
GlyTouCan:  G05704WW
GlyCosmos:  G05704WW
GlyGen:  G05704WW
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
F, H, J, L
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
DA [auth C],
IA [auth D],
X [auth B]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
CA [auth C],
Q [auth A],
R [auth A],
W [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
EA [auth D]
GA [auth D]
HA [auth D]
AA [auth C],
BA [auth C],
EA [auth D],
GA [auth D],
HA [auth D],
M [auth A],
O [auth A],
P [auth A],
S [auth B],
U [auth B],
V [auth B],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
FA [auth D],
N [auth A],
T [auth B],
Z [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary