3U0E

Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with fragment 9320


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

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Ligand Structure Quality Assessment 


This is version 1.1 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.

(2019) Proteins 

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

  • 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 ...

    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

    School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-ketoacyl synthaseA428Brucella 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
07K (Subject of Investigation/LOI)
Query on 07K

Download Ideal Coordinates CCD File 
E [auth A]8-methylquinolin-4-amine
C10 H10 N2
TVZPXEZTWRAIID-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A], D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.07α = 90
b = 83.75β = 121.5
c = 73.61γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references