5NHE

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Cd2+ ions and xylose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.

Lee, M.Rozeboom, H.J.de Waal, P.P.de Jong, R.M.Dudek, H.M.Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

  • DOI: https://doi.org/10.1021/acs.biochem.7b00777
  • Primary Citation of Related Structures:  
    5NH4, 5NH5, 5NH6, 5NH7, 5NH8, 5NH9, 5NHA, 5NHB, 5NHC, 5NHD, 5NHE, 5NHM

  • PubMed Abstract: 

    Xylose isomerase from Piromyces sp. E2 (PirXI) can be used to equip Saccharomyces cerevisiae with the capacity to ferment xylose to ethanol. The biochemical properties and structure of the enzyme have not been described even though its metal content, catalytic parameters, and expression level are critical for rapid xylose utilization. We have isolated the enzyme after high-level expression in Escherichia coli, analyzed the metal dependence of its catalytic properties, and determined 12 crystal structures in the presence of different metals, substrates, and substrate analogues. The activity assays revealed that various bivalent metals can activate PirXI for xylose isomerization. Among these metals, Mn 2+ is the most favorable for catalytic activity. Furthermore, the enzyme shows the highest affinity for Mn 2+ , which was established by measuring the activation constants (K act ) for different metals. Metal analysis of the purified enzyme showed that in vivo the enzyme binds a mixture of metals that is determined by metal availability as well as affinity, indicating that the native metal composition can influence activity. The crystal structures show the presence of an active site similar to that of other xylose isomerases, with a d-xylose binding site containing two tryptophans and a catalytic histidine, as well as two metal binding sites that are formed by carboxylate groups of conserved aspartates and glutamates. The binding positions and conformations of the metal-coordinating residues varied slightly for different metals, which is hypothesized to contribute to the observed metal dependence of the isomerase activity.


  • Organizational Affiliation

    Biochemical 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): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYS
Query on XYS

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
I [auth A]
R [auth B]
X [auth C]
EA [auth D],
FA [auth D],
I [auth A],
R [auth B],
X [auth C],
Z [auth C]
alpha-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
XYP
Query on XYP

Download Ideal Coordinates CCD File 
AA [auth C]
GA [auth D]
H [auth A]
J [auth A]
K [auth A]
AA [auth C],
GA [auth D],
H [auth A],
J [auth A],
K [auth A],
Q [auth B],
S [auth B],
Y [auth C]
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
XLS
Query on XLS

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]
D-xylose
C5 H10 O5
PYMYPHUHKUWMLA-VPENINKCSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
E [auth A]
F [auth A]
N [auth B]
CA [auth D],
DA [auth D],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
V [auth C],
W [auth C]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth C]
HA [auth D]
IA [auth D]
JA [auth D]
L [auth A]
BA [auth C],
HA [auth D],
IA [auth D],
JA [auth D],
L [auth A],
M [auth A],
T [auth B],
U [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.64α = 115.37
b = 79.37β = 89.97
c = 92.01γ = 117.16
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references
  • Version 1.3: 2018-08-29
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary