8B8E

Wild-type GH11 from Blastobotrys mokoenaii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Yeasts Have Evolved Divergent Enzyme Strategies To Deconstruct and Metabolize Xylan.

Ravn, J.L., Ristinmaa, A.S., Coleman, T., Larsbrink, J., Geijer, C.

(2023) Microbiol Spectr : e0024523-e0024523

  • DOI: https://doi.org/10.1128/spectrum.00245-23
  • Primary Citation of Related Structures:  
    8B8E

  • PubMed Abstract: 

    • Together with bacteria and filamentous fungi, yeasts actively take part in the global carbon cycle. Over 100 yeast species have been shown to grow on the major plant polysaccharide xylan, which requires an arsenal of carbohydrate active enzymes. However, which enzymatic strategies yeasts use to deconstruct xylan and what specific biological roles they play in its conversion remain unclear ...

    Together with bacteria and filamentous fungi, yeasts actively take part in the global carbon cycle. Over 100 yeast species have been shown to grow on the major plant polysaccharide xylan, which requires an arsenal of carbohydrate active enzymes. However, which enzymatic strategies yeasts use to deconstruct xylan and what specific biological roles they play in its conversion remain unclear. In fact, genome analyses reveal that many xylan-metabolizing yeasts lack expected xylanolytic enzymes. Guided by bioinformatics, we have here selected three xylan-metabolizing ascomycetous yeasts for in-depth characterization of growth behavior and xylanolytic enzymes. The savanna soil yeast Blastobotrys mokoenaii displays superior growth on xylan thanks to an efficient secreted glycoside hydrolase family 11 (GH11) xylanase; solving its crystal structure revealed a high similarity to xylanases from filamentous fungi. The termite gut-associated Scheffersomyces lignosus, in contrast grows more slowly, and its xylanase activity was found to be mainly cell surface-associated. The wood-isolated Wickerhamomyces canadensis, surprisingly, could not utilize xylan as the sole carbon source without the addition of xylooligosaccharides or exogenous xylanases or even co-culturing with B. mokoenaii , suggesting that W. canadensis relies on initial xylan hydrolysis by neighboring cells. Furthermore, our characterization of a novel W. canadensis GH5 subfamily 49 (GH5_49) xylanase represents the first demonstrated activity in this subfamily. Our collective results provide new information on the variable xylanolytic systems evolved by yeasts and their potential roles in natural carbohydrate conversion. IMPORTANCE Microbes that take part in the degradation of the polysaccharide xylan, the major hemicellulose component in plant biomass, are equipped with specialized enzyme machineries to hydrolyze the polymer into monosaccharides for further metabolism. However, despite being found in virtually every habitat, little is known of how yeasts break down and metabolize xylan and what biological role they may play in its turnover in nature. Here, we have explored the enzymatic xylan deconstruction strategies of three underexplored yeasts from diverse environments, Blastobotrys mokoenaii from soil, Scheffersomyces lignosus from insect guts, and Wickerhamomyces canadensis from trees, and we show that each species has a distinct behavior regarding xylan conversion. These findings may be of high relevance for future design and development of microbial cell factories and biorefineries utilizing renewable plant biomass.

    Organizational Affiliation: 

    Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BmGH11A, B, C, D, E225Blastobotrys mokoenaiiMutation(s): 0 
EC: 3.2.1.8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE
Download Ideal Coordinates CCD File 
J [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
144
Query on 144
Download Ideal Coordinates CCD File 
V [auth B]TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
CA [auth C],
H [auth A],
LA [auth E],
T [auth B]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
FA [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
JA [auth E],
KA [auth E],
P [auth B],
R [auth B],
U [auth B],
JA [auth E],
KA [auth E],
P [auth B],
R [auth B],
U [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
AA [auth C],
BA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
G [auth A],
I [auth A],
IA [auth E],
K [auth A],
L [auth A],
M [auth A],
MA [auth E],
N [auth A],
Q [auth B],
S [auth B],
X [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
GA [auth D],
HA [auth D],
NA [auth E],
O [auth A],
Z [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.039α = 90
b = 37.86β = 104.27
c = 142.609γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Carl Trygger FoundationSwedenCTS 19:195
Carl Trygger FoundationSwedenCTS 18:118
European Union (EU)European Union964430

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release