6T8F

Crystal structure of mutant xylose isomerase (V270A/A273G) from Piromyces E2 grown in yeast, in complex with xylose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance.

Lee, M.Rozeboom, H.J.Keuning, E.de Waal, P.Janssen, D.B.

(2020) Biotechnol Biofuels 13: 5-5

  • DOI: https://doi.org/10.1186/s13068-019-1643-0
  • Primary Citation of Related Structures:  
    6T8E, 6T8F

  • PubMed Abstract: 

    Efficient bioethanol production from hemicellulose feedstocks by Saccharomyces cerevisiae requires xylose utilization. Whereas S. cerevisiae does not metabolize xylose, engineered strains that express xylose isomerase can metabolize xylose by converting it to xylulose. For this, the type II xylose isomerase from Piromyces (PirXI) is used but the in vivo activity is rather low and very high levels of the enzyme are needed for xylose metabolism. In this study, we explore the use of protein engineering and in vivo selection to improve the performance of PirXI. Recently solved crystal structures were used to focus mutagenesis efforts. We constructed focused mutant libraries of Piromyces xylose isomerase by substitution of second shell residues around the substrate- and metal-binding sites. Following library transfer to S. cerevisiae and selection for enhanced xylose-supported growth under aerobic and anaerobic conditions, two novel xylose isomerase mutants were obtained, which were purified and subjected to biochemical and structural analysis. Apart from a small difference in response to metal availability, neither the new mutants nor mutants described earlier showed significant changes in catalytic performance under various in vitro assay conditions. Yet, in vivo performance was clearly improved. The enzymes appeared to function suboptimally in vivo due to enzyme loading with calcium, which gives poor xylose conversion kinetics. The results show that better in vivo enzyme performance is poorly reflected in kinetic parameters for xylose isomerization determined in vitro with a single type of added metal. This study shows that in vivo selection can identify xylose isomerase mutants with only minor changes in catalytic properties measured under standard conditions. Metal loading of xylose isomerase expressed in yeast is suboptimal and strongly influences kinetic properties. Metal uptake, distribution and binding to xylose isomerase are highly relevant for rapid xylose conversion and may be an important target for optimizing yeast xylose metabolism.


  • Organizational Affiliation

    1Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase
A, B, C, D
437Piromyces sp. E2Mutation(s): 2 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for Q9P8C9 (Piromyces sp. (strain E2))
Explore Q9P8C9 
Go to UniProtKB:  Q9P8C9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P8C9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYS
Query on XYS

Download Ideal Coordinates CCD File 
FA [auth D]
GA [auth D]
I [auth A]
J [auth A]
Q [auth B]
FA [auth D],
GA [auth D],
I [auth A],
J [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C]
alpha-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
XYP
Query on XYP

Download Ideal Coordinates CCD File 
EA [auth D]
H [auth A]
HA [auth D]
P [auth B]
X [auth C]
EA [auth D],
H [auth A],
HA [auth D],
P [auth B],
X [auth C],
Z [auth C]
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
XLS
Query on XLS

Download Ideal Coordinates CCD File 
DA [auth D],
G [auth A],
O [auth B],
W [auth C]
D-xylose
C5 H10 O5
PYMYPHUHKUWMLA-VPENINKCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
IA [auth D]
JA [auth D]
K [auth A]
L [auth A]
AA [auth C],
IA [auth D],
JA [auth D],
K [auth A],
L [auth A],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
E [auth A]
F [auth A]
M [auth B]
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
M [auth B],
N [auth B],
U [auth C],
V [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.598α = 115.46
b = 79.372β = 89.98
c = 91.982γ = 117.13
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 2.2: 2024-01-24
    Changes: Data collection, Refinement description