6EHN

Structural insight into a promiscuous CE15 esterase from the marine bacterial metagenome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report



Literature

Structural insight into a CE15 esterase from the marine bacterial metagenome.

De Santi, C.Gani, O.A.Helland, R.Williamson, A.

(2017) Sci Rep 7: 17278-17278

  • DOI: 10.1038/s41598-017-17677-4
  • Primary Citation of Related Structures:  
    6EHN

  • PubMed Abstract: 
  • The family 15 carbohydrate esterase (CE15) MZ0003, which derives from a marine Arctic metagenome, has a broader substrate scope than other members of this family. Here we report the crystal structure of MZ0003, which reveals that residues comprising ...

    The family 15 carbohydrate esterase (CE15) MZ0003, which derives from a marine Arctic metagenome, has a broader substrate scope than other members of this family. Here we report the crystal structure of MZ0003, which reveals that residues comprising the catalytic triad differ from previously-characterized fungal homologs, and resolves three large loop regions that are unique to this bacterial sub-clade. The catalytic triad of the bacterial CE15, which includes Asp 332 as its third member, closely resembles that of family 1 carbohydrate esterases (CE1), despite the overall lower structural similarity with members of this family. Two of the three loop regions form a subdomain that deepens the active site pocket and includes several basic residues that contribute to the high positive charge surrounding the active site. Docking simulations predict specific interactions with the sugar moiety of glucuronic-acid substrates, and with aromatically-substituted derivatives that serve as model compounds for the lignin-carbohydrate complex of plant cell walls. Molecular dynamics simulations indicate considerable flexibility of the sub-domain in the substrate-bound form, suggesting plasticity to accommodate different substrates is possible. The findings from this first reported structure of a bacterial member of the CE15 family provide insight into the basis of its broader substrate specificity.


    Organizational Affiliation

    Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway. adele.williamson@uit.no.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbohydrate esterase MZ0003A399unidentified prokaryotic organismMutation(s): 0 
Gene Names: MZ0003
EC: 3.1.1
Find proteins for A0A0K2VM55 (Unknown prokaryotic organism)
Explore A0A0K2VM55 
Go to UniProtKB:  A0A0K2VM55
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.212α = 90
b = 110.212β = 90
c = 78.666γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
SOLVEphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway247732
Research Council of NorwayNorway--

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release