4TQ5

Structure of a UbiA homolog from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.289 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.6 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
prenyltransferase303Archaeoglobus 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
B [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.289 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.922α = 90
b = 61.922β = 90
c = 248.752γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BOGClick on this verticalbar to view details

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, Structure summary
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.6: 2024-11-20
    Changes: Structure summary