5Z2R

ThDP-Mn2+ complex of R395K variant of EcMenD soaked with 2-ketoglutarate for 5 min


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.

Qin, M.M.Song, H.G.Dai, X.Chen, Y.Z.Guo, Z.H.

(2018) Biochem J 475: 3651-3667

  • DOI: https://doi.org/10.1042/BCJ20180548
  • Primary Citation of Related Structures:  
    5EJM, 5Z2P, 5Z2R, 5Z2U

  • PubMed Abstract: 

    The bacterial enzyme MenD, or 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase, catalyzes an essential Stetter reaction in menaquinone (vitamin K2) biosynthesis via thiamine diphosphate (ThDP)-bound tetrahedral post-decarboxylation intermediates. The detailed mechanism of this intermediate chemistry, however, is still poorly understood, but of significant interest given that menaquinone is an essential electron transporter in many pathogenic bacteria. Here, we used site-directed mutagenesis, enzyme kinetic assays, and protein crystallography to reveal an active-inactive intermediate equilibrium in MenD catalysis and its modulation by two conserved active site arginine residues. We observed that these conserved residues play a key role in shifting the equilibrium to the active intermediate by orienting the C 2 -succinyl group of the intermediates through strong ionic hydrogen bonding. We found that when this interaction is moderately weakened by amino acid substitutions, the resulting proteins are catalytically competent with the C 2 -succinyl group taking either the active or the inactive orientation in the post-decarboxylation intermediate. When this hydrogen-bonding interaction was strongly weakened, the succinyl group was re-oriented by 180° relative to the native intermediate, resulting in the reversal of the stereochemistry at the reaction center that disabled catalysis. Interestingly, this inactive intermediate was formed with a distinct kinetic behavior, likely as a result of a non-native mode of enzyme-substrate interaction. The mechanistic insights gained from these findings improve our understanding of the new ThDP-dependent catalysis. More importantly, the non-native-binding site of the inactive MenD intermediate uncovered here provides a new target for the development of antibiotics.


  • Organizational Affiliation

    Department of Chemistry, 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): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TD6
Query on TD6

Download Ideal Coordinates CCD File 
AB [auth H]
I [auth A]
N [auth B]
OA [auth F]
R [auth C]
AB [auth H],
I [auth A],
N [auth B],
OA [auth F],
R [auth C],
UA [auth G],
Y [auth D]
(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
RWCNVMPVYGBSHH-LBPRGKRZSA-N
TPP
Query on TPP

Download Ideal Coordinates CCD File 
MA [auth E]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A],
NA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

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VA [auth G]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
FMT
Query on FMT

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AA [auth D]
BA [auth D]
CA [auth D]
CB [auth H]
DA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
CB [auth H],
DA [auth D],
EA [auth D],
FA [auth D],
HA [auth E],
IA [auth E],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
P [auth B],
Q [auth B],
QA [auth F],
RA [auth F],
SA [auth F],
T [auth C],
TA [auth F],
U [auth C],
V [auth C],
W [auth C],
WA [auth G],
X [auth C],
XA [auth G],
YA [auth G],
ZA [auth G]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth H]
GA [auth E]
J [auth A]
O [auth B]
PA [auth F]
BB [auth H],
GA [auth E],
J [auth A],
O [auth B],
PA [auth F],
S [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.63α = 82.91
b = 90.75β = 75.71
c = 172.37γ = 64.2
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 2.0: 2021-08-18
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Refinement description