6O9A

Crystal structure of MqnA complexed with 3-hydroxybenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb6O9A/pdb

• Classification: LYASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-13 Released: 2019-04-03 
• Deposition Author(s): Hicks, K.A., Mahanta, N., Naseem, S., Fedoseyenko, D., Begley, T.P., Ealick, S.E.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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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 

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

• PubMed: 30855131 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.59 kDa 
• Atom Count: 4,239 
• Modelled Residue Count: 542 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate dehydratase	A, B	314	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3HB (Subject of Investigation/LOI)	D [auth A], F [auth B]	3-HYDROXYBENZOIC ACID C7 H6 O3 IJFXRHURBJZNAO-UHFFFAOYSA-N
ACT	C [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 = 143.102	α = 90
b = 151.619	β = 90
c = 75.035	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Hicks, K.A., Mahanta, N., Naseem, S., Fedoseyenko, D., Begley, T.P., Ealick, S.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	DK067081

Revision History  

• 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