6HM1

Structural and thermodynamic signatures of ligand binding to an enigmatic chitinase-D from Serratia proteamaculans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structural and Thermodynamic Signatures of Ligand Binding to the Enigmatic Chitinase D of Serratia proteamaculans.

Madhuprakash, J.Dalhus, B.Vaaje-Kolstad, G.Sakuda, S.Podile, A.R.Eijsink, V.G.H.Sorlie, M.

(2019) J Phys Chem B 123: 2270-2279

  • DOI: https://doi.org/10.1021/acs.jpcb.8b11448
  • Primary Citation of Related Structures:  
    6HM1

  • PubMed Abstract: 

    The Gram-negative bacteria Serratia marcescens and Serratia proteamaculans have efficient chitinolytic machineries that degrade chitin into N-acetylglucosamine (GlcNAc), which is used as a carbon and energy source. The enzymatic degradation of chitin in these bacteria occurs through the synergistic action of glycoside hydrolases (GHs) that have complementary activities; an endo-acting GH (ChiC) making random scissions on the polysaccharide chains and two exo-acting GHs mainly targeting single reducing (ChiA) and nonreducing (ChiB) chain ends. Both bacteria produce low amounts of a fourth GH18 (ChiD) with an unclear role in chitin degradation. Here, we have determined the thermodynamic signatures for binding of (GlcNAc) 6 and the inhibitor allosamidin to SpChiD as well as the crystal structure of SpChiD in complex with allosamidin. The binding free energies for the two ligands are similar (Δ G r ° = -8.9 ± 0.1 and -8.4 ± 0.1 kcal/mol, respectively) with clear enthalpic penalties (Δ H r ° = 3.2 ± 0.1 and 1.8 ± 0.1 kcal/mol, respectively). Binding of (GlcNAc) 6 is dominated by solvation entropy change (- TΔ S solv ° = -17.4 ± 0.4 kcal/mol) and the conformational entropy change dominates for allosamidin binding (- TΔ S conf ° = -9.0 ± 0.2 kcal/mol). These signatures as well as the interactions with allosamidin are very similar to those of SmChiB suggesting that both enzymes are nonreducing end-specific.


  • Organizational Affiliation

    Department of Chemistry, Biotechnology and Food Science , NMBU-Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 18400Serratia proteamaculans 568Mutation(s): 0 
Gene Names: Spro_2725
UniProt
Find proteins for A8GFD6 (Serratia proteamaculans (strain 568))
Explore A8GFD6 
Go to UniProtKB:  A8GFD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8GFD6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.777α = 90
b = 62.855β = 90
c = 103.183γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway221576, 247001 and 247730
Norway2015095
IndiaIFA16-LSPA 40

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 2.0: 2019-03-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary