5Z6T

Crystal structure of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insight intoD-xylose utilization by xylose reductase from Scheffersomyces stipitis

Son, H.F.Lee, S.M.Kim, K.J.

(2018) Sci Rep 8: 17442-17442

  • DOI: 10.1038/s41598-018-35703-x
  • Primary Citation of Related Structures:  
    5Z6T, 5Z6U

  • PubMed Abstract: 
  • Lignocellulosic biomass, of which D -xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D -xylose utilization, we determined the crystal structure of D -xylose reductase from Schefferzomyces stipitis (SsXR) at a 1 ...

    Lignocellulosic biomass, of which D -xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D -xylose utilization, we determined the crystal structure of D -xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 Å resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.


    Organizational Affiliation

    KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea. kkim@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-dependent D-xylose reductaseA, B343Scheffersomyces stipitis CBS 6054Mutation(s): 0 
Gene Names: XYL1PICST_89614
EC: 1.1.1.307
UniProt
Find proteins for P31867 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545))
Explore P31867 
Go to UniProtKB:  P31867
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.654α = 90
b = 97.654β = 90
c = 160.119γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-01-25 
  • Released Date: 2018-12-05 
  • Deposition Author(s): Son, H.F., Kim, K.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2020-09-09
    Changes: Structure summary