4TQ6

Structure of a UbiA homolog from Archaeoglobus fulgidus bound to Cd2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1.

Huang, H.Levin, E.J.Liu, S.Bai, Y.Lockless, S.W.Zhou, M.

(2014) PLoS Biol 12: e1001911-e1001911

  • DOI: https://doi.org/10.1371/journal.pbio.1001911
  • Primary Citation of Related Structures:  
    4TQ3, 4TQ4, 4TQ5, 4TQ6

  • PubMed Abstract: 

    Membrane-embedded prenyltransferases from the UbiA family catalyze the Mg2+-dependent transfer of a hydrophobic polyprenyl chain onto a variety of acceptor molecules and are involved in the synthesis of molecules that mediate electron transport, including Vitamin K and Coenzyme Q. In humans, missense mutations to the protein UbiA prenyltransferase domain-containing 1 (UBIAD1) are responsible for Schnyder crystalline corneal dystrophy, which is a genetic disease that causes blindness. Mechanistic understanding of this family of enzymes has been hampered by a lack of three-dimensional structures. We have solved structures of a UBIAD1 homolog from Archaeoglobus fulgidus, AfUbiA, in an unliganded form and bound to Mg2+ and two different isoprenyl diphosphates. Functional assays on MenA, a UbiA family member from E. coli, verified the importance of residues involved in Mg2+ and substrate binding. The structural and functional studies led us to propose a mechanism for the prenyl transfer reaction. Disease-causing mutations in UBIAD1 are clustered around the active site in AfUbiA, suggesting the mechanism of catalysis is conserved between the two homologs.


  • Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
prenyltransferase
A, B
303Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF_1648
Membrane Entity: Yes 
UniProt
Find proteins for O28625 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28625 
Go to UniProtKB:  O28625
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28625
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.938α = 90
b = 89.871β = 90
c = 341.23γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK088057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098878
American Heart AssociationUnited States12EIA8850017
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesR12MZ

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description