The type III pullulan hydrolase from Thermococcus kodakarensis

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

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This is version 1.2 of the entry. See complete history


Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis.

Guo, J.Coker, A.R.Wood, S.P.Cooper, J.B.Keegan, R.M.Ahmad, N.Muhammad, M.A.Rashid, N.Akhtar, M.

(2018) Acta Crystallogr D Struct Biol 74: 305-314

  • DOI: https://doi.org/10.1107/S2059798318001754
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both α-1,4- and α-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95-100°C and has a pH optimum in the range 3.5-4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 Å and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine.

  • Organizational Affiliation

    Division of Medicine, University College London, Gower Street, London WC1E 6BT, England.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pullulanase type II, GH13 family765Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK0977
Find proteins for Q5JID9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JID9 
Go to UniProtKB:  Q5JID9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JID9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.649α = 90
b = 63.888β = 93.8
c = 56.122γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
DIALSdata reduction
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description