4RHF

Crystal structure of UbiX mutant V47S from Colwellia psychrerythraea 34H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes.

Do, H.Kim, S.J.Lee, C.W.Kim, H.W.Park, H.H.Kim, H.M.Park, H.Park, H.Lee, J.H.

(2015) Sci Rep 5: 8196-8196

  • DOI: 10.1038/srep08196
  • Primary Citation of Related Structures:  
    4RHE, 4RHF

  • PubMed Abstract: 
  • The ubiX gene of Colwellia psychrerythraea strain 34H encodes a 3-octaprenyl-4-hydroxybenzoate carboxylase (CpsUbiX, UniProtKB code: Q489U8) that is involved in the third step of the ubiquinone biosynthesis pathway and harbors a flavin mononucleotide (FMN) as a potential cofactor ...

    The ubiX gene of Colwellia psychrerythraea strain 34H encodes a 3-octaprenyl-4-hydroxybenzoate carboxylase (CpsUbiX, UniProtKB code: Q489U8) that is involved in the third step of the ubiquinone biosynthesis pathway and harbors a flavin mononucleotide (FMN) as a potential cofactor. Here, we report the crystal structures of two forms of CpsUbiX: an FMN-bound wild type form and an FMN-unbound V47S mutant form. CpsUbiX is a dodecameric enzyme, and each monomer possesses a typical Rossmann-fold structure. The FMN-binding domain of UbiX is composed of three neighboring subunits. The highly conserved Gly15, Ser41, Val47, and Tyr171 residues play important roles in FMN binding. Structural comparison of the FMN-bound wild type form with the FMN-free form reveals a significant conformational difference in the C-terminal loop region (comprising residues 170-176 and 195-206). Subsequent computational modeling and liposome binding assay both suggest that the conformational flexibility observed in the C-terminal loops plays an important role in substrate and lipid bindings. The crystal structures presented in this work provide structural framework and insights into the catalytic mechanism of CpsUbiX.


    Organizational Affiliation

    1] Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea [2] Department of Polar Sciences, Korea University of Science and Technology, Incheon 406-840, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-octaprenyl-4-hydroxybenzoate carboxy-lyaseA209Colwellia psychrerythraea 34HMutation(s): 1 
Gene Names: ubiXCPS_0408
EC: 4.1.1 (PDB Primary Data), 2.5.1.129 (UniProt)
UniProt
Find proteins for Q489U8 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681))
Explore Q489U8 
Go to UniProtKB:  Q489U8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ489U8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.6α = 90
b = 97.6β = 90
c = 97.6γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MERLOTphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release