EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate for 2 min

Experimental Data Snapshot

  • Resolution: 1.34 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

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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.

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
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TD6

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BA [auth B]
EC [auth F]
ED [auth H]
FB [auth D]
I [auth A]
BA [auth B],
EC [auth F],
ED [auth H],
FB [auth D],
I [auth A],
OA [auth C],
OC [auth G],
QB [auth E]
(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid
C16 H25 N4 O10 P2 S
Query on TRS

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C4 H12 N O3
Query on GOL

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EA [auth B]
HC [auth F]
HD [auth H]
IB [auth D]
IC [auth F]
EA [auth B],
HC [auth F],
HD [auth H],
IB [auth D],
IC [auth F],
JB [auth D],
JD [auth H],
L [auth A],
M [auth A],
ND [auth H],
RA [auth C],
RC [auth G],
TB [auth E],
ZA [auth C]
C3 H8 O3
Query on EDO

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AD [auth G]
BB [auth C]
BC [auth E]
CB [auth C]
LC [auth F]
AD [auth G],
BB [auth C],
BC [auth E],
CB [auth C],
LC [auth F],
LD [auth H],
MC [auth F],
N [auth A],
NA [auth C],
OB [auth D],
OD [auth H],
R [auth A],
S [auth A],
T [auth A],
TA [auth C],
U [auth A],
V [auth A],
W [auth A],
WA [auth C],
XA [auth C],
XC [auth G]
C2 H6 O2
Query on MN

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CA [auth B]
FC [auth F]
FD [auth H]
GB [auth D]
J [auth A]
CA [auth B],
FC [auth F],
FD [auth H],
GB [auth D],
J [auth A],
PA [auth C],
PC [auth G],
RB [auth E]
Query on FMT

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AA [auth B]
AB [auth C]
AC [auth E]
BD [auth G]
CC [auth E]
AA [auth B],
AB [auth C],
AC [auth E],
BD [auth G],
CC [auth E],
CD [auth G],
DB [auth C],
DC [auth F],
DD [auth H],
EB [auth D],
FA [auth B],
HA [auth B],
IA [auth B],
ID [auth H],
JA [auth B],
JC [auth F],
KA [auth B],
KB [auth D],
KC [auth F],
LA [auth B],
MA [auth B],
MB [auth D],
MD [auth H],
NB [auth D],
NC [auth F],
P [auth A],
PB [auth D],
PD [auth H],
Q [auth A],
TC [auth G],
UB [auth E],
UC [auth G],
VA [auth C],
VB [auth E],
VC [auth G],
WC [auth G],
X [auth A],
XB [auth E],
Y [auth A],
YA [auth C],
YB [auth E],
YC [auth G],
Z [auth A],
ZB [auth E],
ZC [auth G]
C H2 O2
Query on MG

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DA [auth B]
GA [auth B]
GC [auth F]
GD [auth H]
HB [auth D]
DA [auth B],
GA [auth B],
GC [auth F],
GD [auth H],
HB [auth D],
K [auth A],
KD [auth H],
LB [auth D],
O [auth A],
QA [auth C],
QC [auth G],
SB [auth E],
SC [auth G],
UA [auth C],
WB [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.34 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.66α = 83.25
b = 90.76β = 76.03
c = 169.34γ = 64.32
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

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: 2024-03-20
    Changes: Data collection, Database references, Derived calculations