7M66 | pdb_00007m66

Targeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7M66

This is version 1.2 of the entry. See complete history

Literature

Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor.

Bose, S.Steussy, C.N.Lopez-Perez, D.Schmidt, T.Kulathunga, S.C.Seleem, M.N.Lipton, M.Mesecar, A.D.Rodwell, V.W.Stauffacher, C.V.

(2023) Commun Biol 6: 360-360

  • DOI: https://doi.org/10.1038/s42003-023-04639-y
  • Primary Citation Related Structures: 
    7M66

  • PubMed Abstract: 

    HMG-CoA reductase (HMGR), a rate-limiting enzyme of the mevalonate pathway in Gram-positive pathogenic bacteria, is an attractive target for development of novel antibiotics. In this study, we report the crystal structures of HMGR from Enterococcus faecalis (efHMGR) in the apo and liganded forms, highlighting several unique features of this enzyme. Statins, which inhibit the human enzyme with nanomolar affinity, perform poorly against the bacterial HMGR homologs. We also report a potent competitive inhibitor (Chembridge2 ID 7828315 or compound 315) of the efHMGR enzyme identified by a high-throughput, in-vitro screening. The X-ray crystal structure of efHMGR in complex with 315 was determined to 1.27 Å resolution revealing that the inhibitor occupies the mevalonate-binding site and interacts with several key active site residues conserved among bacterial homologs. Importantly, 315 does not inhibit the human HMGR. Our identification of a selective, non-statin inhibitor of bacterial HMG-CoA reductases will be instrumental in lead optimization and development of novel antibacterial drug candidates.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 186.88 kDa 
  • Atom Count: 11,939 
  • Modeled Residue Count: 1,437 
  • Deposited Residue Count: 1,692 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hydroxymethylglutaryl-CoA reductase, degradative
A, B, C, D
423Enterococcus faecalisMutation(s): 0 
Gene Names: EY666_03235
EC: 1.1.1.88 (PDB Primary Data), 2.3.1.9 (UniProt)
UniProt
Find proteins for A0A4U3MLJ4 (Enterococcus faecalis)
Explore A0A4U3MLJ4 
Go to UniProtKB:  A0A4U3MLJ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4U3MLJ4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
AA [auth D],
F [auth A],
M [auth B],
N [auth B],
Z [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
BA [auth D]
G [auth A]
H [auth A]
I [auth A]
V [auth C]
BA [auth D],
G [auth A],
H [auth A],
I [auth A],
V [auth C],
W [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
T [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
O [auth B],
P [auth B],
Q [auth B],
U [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
CA [auth D]
DA [auth D]
EA [auth D]
J [auth A]
K [auth A]
CA [auth D],
DA [auth D],
EA [auth D],
J [auth A],
K [auth A],
L [auth A],
R [auth B],
S [auth B],
X [auth C],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.661α = 90
b = 168.661β = 90
c = 120.194γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL52115

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection