3IM9 | pdb_00003im9

Crystal structure of MCAT from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3IM9/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-10 Released: 2010-06-16 
• Deposition Author(s): Hong, S.K., Kim, K.H., Park, J.K., Kim, Y.M., Kim, E.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.184 (Depositor) 
• R-Value Work: 
  0.157 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

New design platform for malonyl-CoA-acyl carrier protein transacylase

Hong, S.K., Kim, K.H., Park, J.K., Jeong, K.-W., Kim, Y.M., Kim, E.E.

(2010) FEBS Lett 584: 1240-1244

• PubMed: 20176020 
• DOI: https://doi.org/10.1016/j.febslet.2010.02.038
• Primary Citation Related Structures: 
  3IM8, 3IM9


• PubMed Abstract: 
  

  Malonyl-CoA-acyl carrier protein transacylase (MCAT) transfers the malonyl group from malonyl-CoA to holo-acyl carrier protein (ACP), and since malonyl-ACP is a key building block for fatty-acid biosynthesis it is considered as a promising antibacterial target. The crystal structures of MCAT from Staphylococcus aureus and Streptococcus pneumoniae have been determined at 1.46 and 2.1A resolution, respectively. In the SaMCAT structure, the N-terminal expression peptide of a neighboring molecule running in the opposite direction of malonyl-CoA makes extensive interactions with the highly conserved "Gly-Gln-Gly-Ser-Gln" stretch, suggesting a new design platform. Mutagenesis results suggest that Ser91 and His199 are the catalytic dyad.

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Organizational Affiliation: 
• Korea Institute of Science and Technology, Life Sciences Division, Seoul, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 34.68 kDa 
• Atom Count: 2,622 
• Modeled Residue Count: 313 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malonyl CoA-acyl carrier protein transacylase	A	316	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: fabD EC: 2.3.1.39
UniProt
Find proteins for Q99UN8 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99UN8  Go to UniProtKB:  Q99UN8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.184 (Depositor) 
• R-Value Work:  0.157 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.157	α = 90
b = 87.914	β = 104
c = 43.237	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Hong, S.K., Kim, K.H., Park, J.K., Kim, Y.M., Kim, E.E.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description