4OD5

Substrate-bound structure of a UbiA homolog from Aeropyrum pernix K1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.281 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into ubiquinone biosynthesis in membranes.

Cheng, W.Li, W.

(2014) Science 343: 878-881

  • DOI: https://doi.org/10.1126/science.1246774
  • Primary Citation of Related Structures:  
    4OD4, 4OD5

  • PubMed Abstract: 

    Biosynthesis of ubiquinones requires the intramembrane UbiA enzyme, an archetypal member of a superfamily of prenyltransferases that generates lipophilic aromatic compounds. Mutations in eukaryotic superfamily members have been linked to cardiovascular degeneration and Parkinson's disease. To understand how quinones are produced within membranes, we report the crystal structures of an archaeal UbiA in its apo and substrate-bound states at 3.3 and 3.6 angstrom resolution, respectively. The structures reveal nine transmembrane helices and an extramembrane cap domain that surround a large central cavity containing the active site. To facilitate the catalysis inside membranes, UbiA has an unusual active site that opens laterally to the lipid bilayer. Our studies illuminate general mechanisms for substrate recognition and catalysis in the UbiA superfamily and rationalize disease-related mutations in humans.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxybenzoate octaprenyltransferase
A, B, C, D, E
A, B, C, D, E, F
303Aeropyrum pernix K1Mutation(s): 0 
Gene Names: ubiAAPE_1570
EC: 2.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YBM8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YBM8 
Go to UniProtKB:  Q9YBM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YBM8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GST
Query on GST

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
GERANYL S-THIOLODIPHOSPHATE
C10 H20 O6 P2 S
AKIXWSDUEPPMKM-JXMROGBWSA-N
PHB
Query on PHB

Download Ideal Coordinates CCD File 
BA [auth F]
H [auth A]
L [auth B]
P [auth C]
T [auth D]
BA [auth F],
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
I [auth A]
J [auth A]
M [auth B]
CA [auth F],
DA [auth F],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D],
Y [auth E],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.104α = 90
b = 122.829β = 90
c = 423.416γ = 90
Software Package:
Software NamePurpose
RAPDdata collection
DMmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations