Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural and functional analysis of Vitamin K2 synthesis protein MenD.

Priyadarshi, A.Kim, E.E.Hwang, K.Y.

(2009) Biochem Biophys Res Commun 388: 748-751

  • DOI: https://doi.org/10.1016/j.bbrc.2009.08.093
  • Primary Citation of Related Structures:  
    3HWW, 3HWX

  • PubMed Abstract: 

    Here we describe in detail the crystal structures of the Vitamin K(2) synthesis protein MenD, from Escherichia coli, in complex with thiamine diphosphate (ThDP) and oxoglutarate, and the effects of cofactor and substrate on its structural stability. This is the first reported structure of MenD in complex with oxoglutarate. The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure. Biospecific-interaction analysis using surface plasmon resonance (SPR) technology reveals an affinity for ThDP and oxoglutarate in the nanomolar range. Biochemical and structural analysis confirmed that MenD is highly dependent on ThDP for its structural stability. Our structural results combined with the biochemical assay reveal novel features of the enzyme that could be utilized in a program of rational structure-based drug design, as well as in helping to enhance our knowledge of the menaquinone synthesis pathway in greater detail.

  • Organizational Affiliation

    Biomedical Research Center, Korea Institute of Science and Technology, Seoul 136-791, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase556Escherichia coli K-12Mutation(s): 1 
Gene Names: b2264JW5374menD
Find proteins for P17109 (Escherichia coli (strain K12))
Explore P17109 
Go to UniProtKB:  P17109
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17109
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TPP

Download Ideal Coordinates CCD File 
AA [auth R]
FA [auth S]
HA [auth Z]
K [auth A]
LA [auth 1]
AA [auth R],
FA [auth S],
HA [auth Z],
K [auth A],
LA [auth 1],
N [auth B],
S [auth I],
V [auth J]
C12 H19 N4 O7 P2 S
Query on GOL

Download Ideal Coordinates CCD File 
OA [auth 1],
U [auth J]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
BA [auth R]
GA [auth S]
IA [auth Z]
L [auth A]
MA [auth 1]
BA [auth R],
GA [auth S],
IA [auth Z],
L [auth A],
MA [auth 1],
O [auth B],
T [auth I],
W [auth J]
Query on NA

Download Ideal Coordinates CCD File 
CA [auth S]
DA [auth S]
EA [auth S]
I [auth A]
J [auth A]
CA [auth S],
DA [auth S],
EA [auth S],
I [auth A],
J [auth A],
JA [auth Z],
KA [auth Z],
M [auth B],
NA [auth 1],
P [auth I],
Q [auth I],
R [auth I],
X [auth R],
Y [auth R],
Z [auth R]
Binding Affinity Annotations 
IDSourceBinding Affinity
TPP PDBBind:  3HWX Kd: 13.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.353α = 75.99
b = 90.463β = 83
c = 169.17γ = 64.15
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description