Cycloalternan-degrading enzyme from Trueperella pyogenes in complex with cycloalternan

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity.

Light, S.H.Cahoon, L.A.Mahasenan, K.V.Lee, M.Boggess, B.Halavaty, A.S.Mobashery, S.Freitag, N.E.Anderson, W.F.

(2017) Structure 25: 295-304

  • DOI: https://doi.org/10.1016/j.str.2016.12.007
  • Primary Citation of Related Structures:  
    5HOP, 5HPO, 5HXM, 5I0D, 5I0E, 5I0F, 5I0G

  • PubMed Abstract: 

    Active in the aqueous cellular environment where a massive excess of water is perpetually present, enzymes that catalyze the transfer of an electrophile to a non-water nucleophile (transferases) require specific strategies to inhibit mechanistically related hydrolysis reactions. To identify principles that confer transferase versus hydrolase reaction specificity, we exploited two enzymes that use highly similar catalytic apparatuses to catalyze the transglycosylation (a transferase reaction) or hydrolysis of α-1,3-glucan linkages in the cyclic tetrasaccharide cycloalternan (CA). We show that substrate binding to non-catalytic domains and a conformationally stable active site promote CA transglycosylation, whereas a distinct pattern of active site conformational change is associated with CA hydrolysis. These findings defy the classic view of induced-fit conformational change and illustrate a mechanism by which a stable hydrophobic binding site can favor transferase activity and disfavor hydrolysis. Application of these principles could facilitate the rational reengineering of transferases with desired catalytic properties.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 31A [auth B]733Trueperella pyogenesMutation(s): 1 
Gene Names: CQ11_05330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranoseB [auth A]4N/A
Glycosylation Resources
GlyTouCan:  G67006KT
GlyCosmos:  G67006KT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SIN

Download Ideal Coordinates CCD File 
C4 H6 O4
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.368α = 90
b = 103.9β = 90.32
c = 44.798γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary