5KDR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 c ...

    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.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.,Northeastern Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
A
327Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: accA
EC: 2.1.3.15
Find proteins for Q2FXM7 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXM7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
B
285Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: accD
EC: 2.1.3.15
Find proteins for Q2FXM6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXM6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
YT5
Query on YT5

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Download CCD File 
B
Moiramide B
(2~{E},4~{E})-~{N}-[(1~{S})-3-[[(2~{S})-3-methyl-1-[(3~{R},4~{S})-4-methyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-1-phenyl-propyl]hexa-2,4-dienamide
C25 H31 N3 O5
WMLLJSBRSSYYPT-PQUJRENYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.807α = 90.00
b = 49.445β = 91.94
c = 100.048γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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