5KDR

The crystal structure of carboxyltransferase from Staphylococcus Aureus bound to the antimicrobial agent moiramide B.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

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Literature

Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B.

Silvers, M.A., Pakhomova, S., Neau, D.B., Silvers, W.C., Anzalone, N., Taylor, C.M., Waldrop, G.L.

(2016) Biochemistry 55: 4666-4674

  • DOI: 10.1021/acs.biochem.6b00641
  • Primary Citation of Related Structures:  
    5KDR

  • PubMed Abstract: 

    • The dramatic increase in the prevalence of antibiotic-resistant bacteria has necessitated a search for new antibacterial agents against novel targets. Moiramide B is a natural product, broad-spectrum antibiotic that inhibits the carboxyltransferase component of acetyl-CoA carboxylase, which catalyzes the first committed step in fatty acid synthesis ...

    The dramatic increase in the prevalence of antibiotic-resistant bacteria has necessitated a search for new antibacterial agents against novel targets. Moiramide B is a natural product, broad-spectrum antibiotic that inhibits the carboxyltransferase component of acetyl-CoA carboxylase, which catalyzes the first committed step in fatty acid synthesis. Herein, we report the 2.6 Å resolution crystal structure of moiramide B bound to carboxyltransferase. An unanticipated but significant finding was that moiramide B bound as the enol/enolate. Crystallographic studies demonstrate that the (4S)-methyl succinimide moiety interacts with the oxyanion holes of the enzyme, supporting the notion that an anionic enolate is the active form of the antibacterial agent. Structure-activity studies demonstrate that the unsaturated fatty acid tail of moiramide B is needed only for entry into the bacterial cell. These results will allow the design of new antibacterial agents against the bacterial form of carboxyltransferase.

    Organizational Affiliation: 

    Department of Radiology, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-coenzyme A carboxylase carboxyl transferase subunit alphaA327Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
Gene Names: accA, SAUSA300_1646
EC: 6.4.1.2 (PDB Primary Data), 2.1.3.15 (UniProt)
UniProt
Find proteins for Q2FXM7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXM7 
Go to UniProtKB:  Q2FXM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXM7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-coenzyme A carboxylase carboxyl transferase subunit betaB285Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: accD, SAB1559c
EC: 6.4.1.2 (PDB Primary Data), 2.1.3.15 (UniProt)
UniProt
Find proteins for Q2FXM6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXM6 
Go to UniProtKB:  Q2FXM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXM6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YT5
Query on YT5
Download Ideal Coordinates CCD File 
E [auth B]Moiramide B
C25 H31 N3 O5
WMLLJSBRSSYYPT-PQUJRENYSA-N		 Ligand Interaction
SO4
Query on SO4
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C [auth A],
D [auth A],
F [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
H [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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G [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.807α = 90
b = 49.445β = 91.94
c = 100.048γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references