6T0I

The wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with the aldotetrauronic acid XUX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical studies of the glucuronoyl esteraseOtCE15A illuminate its interaction with lignocellulosic components.

Mazurkewich, S.Poulsen, J.N.Lo Leggio, L.Larsbrink, J.

(2019) J Biol Chem 294: 19978-19987

  • DOI: 10.1074/jbc.RA119.011435
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages between lignin and glucuronic acid moieties on glucuronoxylan in plant biomass. As such, GEs represent promising biochemical tools in industrial processing of these recalcitrant reso ...

    Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages between lignin and glucuronic acid moieties on glucuronoxylan in plant biomass. As such, GEs represent promising biochemical tools in industrial processing of these recalcitrant resources. However, details on how GEs interact and catalyze degradation of their natural substrates are sparse, calling for thorough enzyme structure-function studies. Presented here is a structural and mechanistic investigation of the bacterial GE Ot CE15A. GEs belong to the carbohydrate esterase family 15 (CE15), which is in turn part of the larger α/β-hydrolase superfamily. GEs contain a Ser-His-Asp/Glu catalytic triad, but the location of the catalytic acid in GEs has been shown to be variable, and Ot CE15A possesses two putative catalytic acidic residues in the active site. Through site-directed mutagenesis, we demonstrate that these residues are functionally redundant, possibly indicating the evolutionary route toward new functionalities within the family. Structures determined with glucuronate, in both native and covalently bound intermediate states, and galacturonate provide insights into the catalytic mechanism of CE15. A structure of Ot CE15A with the glucuronoxylooligosaccharide 2 3 -(4- O -methyl-α-d-glucuronyl)-xylotriose (commonly referred to as XUX) shows that the enzyme can indeed interact with polysaccharides from the plant cell wall, and an additional structure with the disaccharide xylobiose revealed a surface binding site that could possibly indicate a recognition mechanism for long glucuronoxylan chains. Collectively, the results indicate that Ot CE15A, and likely most of the CE15 family, can utilize esters of glucuronoxylooligosaccharides and support the proposal that these enzymes work on lignin-carbohydrate complexes in plant biomass.


    Organizational Affiliation

    Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden johan.larsbrink@chalmers.se.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glucuronoyl esterase OtCE15A
A
421Opitutus terraeMutation(s): 0 
EC: 3.1.1
Find proteins for B1ZMF4 (Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1))
Go to UniProtKB:  B1ZMF4
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCV
Query on GCV

Download CCD File 
A
4-O-METHYL-ALPHA-D-GLUCURONIC ACID
C7 H12 O7
WGLLPAPKWFDHHV-NRGGUMNKSA-N
 Ligand Interaction
XYP
Query on XYP

Download CCD File 
A
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.164 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.406α = 75.8
b = 44.173β = 65.489
c = 50.237γ = 70.984
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Novo Nordisk FoundationDenmarkNNF17OC0027698

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references