5EJ9

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis

Song, H.G.Dong, C.Qin, M.M.Chen, Y.Z.Sun, Y.R.Liu, J.J.Chan, W.Guo, Z.H.

(2016) J Am Chem Soc 138: 7244-7247

  • DOI: https://doi.org/10.1021/jacs.6b03437
  • Primary Citation of Related Structures:  
    5EJ4, 5EJ5, 5EJ6, 5EJ7, 5EJ8, 5EJ9, 5EJA

  • PubMed Abstract: 

    Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.


  • Organizational Affiliation

    Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.


Macromolecules
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 synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
556Escherichia coli K-12Mutation(s): 0 
Gene Names: menDb2264JW5374
EC: 2.2.1.9
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
DA [auth F]
GA [auth G]
I [auth A]
LA [auth H]
N [auth B]
DA [auth F],
GA [auth G],
I [auth A],
LA [auth H],
N [auth B],
Q [auth C],
V [auth D],
Y [auth E]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth E]
FA [auth F]
IA [auth G]
K [auth A]
NA [auth H]
AA [auth E],
FA [auth F],
IA [auth G],
K [auth A],
NA [auth H],
P [auth B],
S [auth C],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
EA [auth F]
HA [auth G]
J [auth A]
MA [auth H]
O [auth B]
EA [auth F],
HA [auth G],
J [auth A],
MA [auth H],
O [auth B],
R [auth C],
W [auth D],
Z [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth F]
JA [auth G]
KA [auth H]
L [auth A]
BA [auth E],
CA [auth F],
JA [auth G],
KA [auth H],
L [auth A],
M [auth B],
T [auth C],
U [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.72α = 76.06
b = 90.72β = 83.35
c = 169.47γ = 64.38
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description