6O9A

Crystal structure of MqnA complexed with 3-hydroxybenzoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Literature

Menaquinone Biosynthesis: Biochemical and Structural Studies of Chorismate Dehydratase.

Mahanta, N., Hicks, K.A., Naseem, S., Zhang, Y., Fedoseyenko, D., Ealick, S.E., Begley, T.P.

(2019) Biochemistry 58: 1837-1840

  • DOI: https://doi.org/10.1021/acs.biochem.9b00105
  • Primary Citation of Related Structures:  
    6O9A

  • PubMed Abstract: 

    Menaquinone (MK, vitamin K) is a lipid-soluble quinone that participates in the bacterial electron transport chain. In mammalian cells, vitamin K functions as an essential vitamin for the activation of several proteins involved in blood clotting and bone metabolism. MqnA is the first enzyme on the futalosine-dependent pathway to menaquinone and catalyzes the aromatization of chorismate by water loss. Here we report biochemical and structural studies of MqnA. These studies suggest that the dehydration reaction proceeds by a variant of the E1cb mechanism in which deprotonation is slower than water loss and that the enol carboxylate of the substrate is serving as the base.

    • Organizational Affiliation: 

    Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chorismate dehydratase
A, B
314Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: mqnA, DR_0370
EC: 4.2.1.151
UniProt
Find proteins for Q9RXE3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RXE3 
Go to UniProtKB:  Q9RXE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RXE3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.102α = 90
b = 151.619β = 90
c = 75.035γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesDK067081

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description