2E1Q

Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate

Yamaguchi, Y.Matsumura, T.Ichida, K.Okamoto, K.Nishino, T.

(2007) J Biochem 141: 513-524

  • DOI: https://doi.org/10.1093/jb/mvm053
  • Primary Citation of Related Structures:  
    2E1Q

  • PubMed Abstract: 

    Xanthine oxidase (oxidoreductase; XOR) and aldehyde oxidase (AO) are similar in protein structure and prosthetic group composition, but differ in substrate preference. Here we show that mutation of two amino acid residues in the active site of human XOR for purine substrates results in conversion of the substrate preference to AO type. Human XOR and its Glu803-to-valine (E803V) and Arg881-to-methionine (R881M) mutants were expressed in an Escherichia coli system. The E803V mutation almost completely abrogated the activity towards hypoxanthine as a substrate, but very weak activity towards xanthine remained. On the other hand, the R881M mutant lacked activity towards xanthine, but retained slight activity towards hypoxanthine. Both mutants, however, exhibited significant aldehyde oxidase activity. The crystal structure of E803V mutant of human XOR was determined at 2.6 A resolution. The overall molybdopterin domain structure of this mutant closely resembles that of bovine milk XOR; amino acid residues in the active centre pocket are situated at very similar positions and in similar orientations, except that Glu803 was replaced by valine, indicating that the decrease in activity towards purine substrate is not due to large conformational change in the mutant enzyme. Unlike wild-type XOR, the mutants were not subject to time-dependent inhibition by allopurinol.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xanthine dehydrogenase/oxidase
A, B, C, D
1,333Homo sapiensMutation(s): 1 
EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P47989 (Homo sapiens)
Explore P47989 
Go to UniProtKB:  P47989
PHAROS:  P47989
GTEx:  ENSG00000158125 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47989
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
BA [auth C],
J [auth A],
KA [auth D],
S [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE
Query on MTE

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CA [auth C],
K [auth A],
LA [auth D],
T [auth B]
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
AA [auth C]
H [auth A]
I [auth A]
IA [auth D]
JA [auth D]
AA [auth C],
H [auth A],
I [auth A],
IA [auth D],
JA [auth D],
Q [auth B],
R [auth B],
Z [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOM
Query on MOM

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DA [auth C],
L [auth A],
MA [auth D],
U [auth B]
HYDROXY(DIOXO)MOLYBDENUM
H Mo O3
WEHYDZQUOLJPRX-UHFFFAOYSA-M
SAL
Query on SAL

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EA [auth C],
M [auth A],
NA [auth D],
V [auth B]
2-HYDROXYBENZOIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
BCT
Query on BCT

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E [auth A],
FA [auth D],
N [auth B],
W [auth C]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
GA [auth D]
HA [auth D]
O [auth B]
F [auth A],
G [auth A],
GA [auth D],
HA [auth D],
O [auth B],
P [auth B],
X [auth C],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SAL BindingDB:  2E1Q Ki: 1.00e+8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.571α = 90
b = 140.944β = 91.49
c = 176.484γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description