4JV3

Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites.

Patterson, E.I.Nanson, J.D.Abendroth, J.Bryan, C.Sankaran, B.Myler, P.J.Forwood, J.K.

(2020) Proteins 88: 47-56

  • DOI: https://doi.org/10.1002/prot.25765
  • Primary Citation of Related Structures:  
    3LRF, 3MQD, 3U0E, 3U0F, 4JV3

  • PubMed Abstract: 

    The bacterial fatty acid pathway is essential for membrane synthesis and a range of other metabolic and cellular functions. The β-ketoacyl-ACP synthases carry out the initial elongation reaction of this pathway, utilizing acetyl-CoA as a primer to elongate malonyl-ACP by two carbons, and subsequent elongation of the fatty acyl-ACP substrate by two carbons. Here we describe the structures of the β-ketoacyl-ACP synthase I from Brucella melitensis in complex with platencin, 7-hydroxycoumarin, and (5-thiophen-2-ylisoxazol-3-yl)methanol. The enzyme is a dimer and based on structural and sequence conservation, harbors the same active site configuration as other β-ketoacyl-ACP synthases. The platencin binding site overlaps with the fatty acyl compound supplied by ACP, while 7-hydroxyl-coumarin and (5-thiophen-2-ylisoxazol-3-yl)methanol bind at the secondary fatty acyl binding site. These high-resolution structures, ranging between 1.25 and 1.70 å resolution, provide a basis for in silico inhibitor screening and optimization, and can aid in rational drug design by revealing the high-resolution binding interfaces of molecules at the malonyl-ACP and acyl-ACP active sites.


  • Organizational Affiliation

    Department of Pathology, University of Texas Medical Branch, Galveston, Texas.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-ketoacyl synthase428Brucella abortus 2308Mutation(s): 0 
Gene Names: fabBBAB1_2173
EC: 2.3.1.41
UniProt
Find proteins for Q2YQQ9 (Brucella abortus (strain 2308))
Explore Q2YQQ9 
Go to UniProtKB:  Q2YQQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YQQ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N32
Query on N32

Download Ideal Coordinates CCD File 
B [auth A]2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid
C24 H27 N O6
DWUHGPPFFABTIY-RLWZQHMASA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSU
Query on CSU
A
L-PEPTIDE LINKINGC3 H7 N O5 S2CYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.16α = 90
b = 84.48β = 120.81
c = 74.02γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Structure summary
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description