2FA3 | pdb_00002fa3

HMG-CoA synthase from Brassica juncea in complex with acetyl-CoA and acetyl-cys117.

• PDB DOI: https://doi.org/10.2210/pdb2FA3/pdb

• Classification: TRANSFERASE
• Organism(s): Brassica juncea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-12-06 Released: 2006-07-25 
• Deposition Author(s): Pojer, F., Ferrer, J.L., Richard, S.B., Noel, J.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.282 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the design of potent and species-specific inhibitors of 3-hydroxy-3-methylglutaryl CoA synthases.

Pojer, F., Ferrer, J.L., Richard, S.B., Nagegowda, D.A., Chye, M.L., Bach, T.J., Noel, J.P.

(2006) Proc Natl Acad Sci U S A 103: 11491-11496

• PubMed: 16864776 
• DOI: https://doi.org/10.1073/pnas.0604935103
• Primary Citation Related Structures: 
  2F82, 2F9A, 2FA0, 2FA3


• PubMed Abstract: 
  

  3-Hydroxy-3-methylglutaryl CoA synthase (HMGS) catalyzes the first committed step in the mevalonate metabolic pathway for isoprenoid biosynthesis and serves as an alternative target for cholesterol-lowering and antibiotic drugs. We have determined a previously undescribed crystal structure of a eukaryotic HMGS bound covalently to a potent and specific inhibitor F-244 [(E,E)-11-[3-(hydroxymethyl)-4-oxo-2-oxytanyl]-3,5,7-trimethyl-2,4-undecadienenoic acid]. Given the accessibility of synthetic analogs of the F-244 natural product, this inhibited eukaryotic HMGS structure serves as a necessary starting point for structure-based methods that may improve the potency and species-specific selectivity of the next generation of F-244 analogs designed to target particular eukaryotic and prokaryotic HMGS.

---

Organizational Affiliation: 
• Howard Hughes Medical Institute, The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 50.88 kDa 
• Atom Count: 3,697 
• Modeled Residue Count: 450 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HMG-CoA synthase	A	450	Brassica juncea	Mutation(s): 1  EC: 2.3.3.10
UniProt
Find proteins for Q9M6U3 (Brassica juncea) Explore Q9M6U3  Go to UniProtKB:  Q9M6U3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	B [auth A]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY	A	L-PEPTIDE LINKING	C5 H9 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.282 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 61.6	β = 90
c = 411.79	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
NEMO	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Pojer, F., Ferrer, J.L., Richard, S.B., Noel, J.P.

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary