1PR9

Human L-Xylulose Reductase Holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human L-xylulose reductase holoenzyme: probing the role of Asn107 with site-directed mutagenesis

El-Kabbani, O.Ishikura, S.Darmanin, C.Carbone, V.Chung, R.P.-T.Usami, N.Hara, A.

(2004) Proteins 55: 724-732

  • DOI: 10.1002/prot.20047

  • PubMed Abstract: 
  • L-Xylulose reductase (XR), an enzyme in the uronate cycle of glucose metabolism, belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. Among the SDR enzymes, XR shows the highest sequence identity (67%) with mouse lung carbonyl reduct ...

    L-Xylulose reductase (XR), an enzyme in the uronate cycle of glucose metabolism, belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. Among the SDR enzymes, XR shows the highest sequence identity (67%) with mouse lung carbonyl reductase (MLCR), but the two enzymes show different substrate specificities. The crystal structure of human XR in complex with reduced nicotinamide adenine dinucleotide phosphate (NADPH) was determined at 1.96 A resolution by using the molecular replacement method and the structure of MLCR as the search model. Features unique to human XR include electrostatic interactions between the N-terminal residues of subunits related by the P-axis, termed according to SDR convention, and an interaction between the hydroxy group of Ser185 and the pyrophosphate of NADPH. Furthermore, identification of the residues lining the active site of XR (Cys138, Val143, His146, Trp191, and Met200) together with a model structure of XR in complex with L-xylulose, revealed structural differences with other members of the SDR family, which may account for the distinct substrate specificity of XR. The residues comprising a recently proposed catalytic tetrad in the SDR enzymes are conserved in human XR (Asn107, Ser136, Tyr149, and Lys153). To examine the role of Asn107 in the catalytic mechanism of human XR, mutant forms (N107D and N107L) were prepared. The two mutations increased K(m) for the substrate (>26-fold) and K(d) for NADPH (95-fold), but only the N107L mutation significantly decreased k(cat) value. These results suggest that Asn107 plays a critical role in coenzyme binding rather than in the catalytic mechanism.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of human L-xylulose reductase
      El-Kabbani, O.,Chung, R.P.-T.,Ishikura, S.,Usami, N.,Nakagawa, J.,Hara, A.
      (2002) Acta Crystallogr.,Sect.D 58: 1379


    Organizational Affiliation

    Department of Medicinal Chemistry, Victorian College of Pharmacy, Monash University (Parkville Campus), Parkville, Victoria, Australia. Ossama.El-Kabbani@vcp.monash.edu.au




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-XYLULOSE REDUCTASE
A, B
244Homo sapiensGene Names: DCXR (SDR20C1)
EC: 1.1.1.10
Find proteins for Q7Z4W1 (Homo sapiens)
Go to Gene View: DCXR
Go to UniProtKB:  Q7Z4W1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
2HP
Query on 2HP

Download SDF File 
Download CCD File 
A, B
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.111α = 90.00
b = 87.938β = 90.00
c = 72.883γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXL-97refinement
X-PLORmodel building
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description