7PPS

apo FabB from Pseudomonas aeruginosa with single point mutation C161A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Pseudomonas aeruginosa FabB C161A, a template for structure-based design for new antibiotics.

Yadrykhins'ky, V.Georgiou, C.Brenk, R.

(2021) F1000Res 10

  • DOI: 10.12688/f1000research.74018.2
  • Primary Citation of Related Structures:  
    7PPS

  • PubMed Abstract: 
  • Background : FabB (3-oxoacyl-[acyl-carrier-protein] synthase 1) is part of the fatty acid synthesis II pathway found in bacteria and a potential target for antibiotics. The enzyme catalyses the Claisen condensation of malonyl-ACP (acyl carrier protein) with acyl-ACP via an acyl-enzyme intermediate ...

    Background : FabB (3-oxoacyl-[acyl-carrier-protein] synthase 1) is part of the fatty acid synthesis II pathway found in bacteria and a potential target for antibiotics. The enzyme catalyses the Claisen condensation of malonyl-ACP (acyl carrier protein) with acyl-ACP via an acyl-enzyme intermediate. Here, we report the crystal structure of the intermediate-mimicking Pseudomonas aeruginosa FabB ( Pa FabB) C161A variant. Methods : His-tagged Pa FabB C161A was expressed in E. coli Rosetta DE3 pLysS cells, cleaved by TEV protease and purified using affinity and size exclusion chromatography. Commercial screens were used to identify suitable crystallization conditions which were subsequently improved to obtain well diffracting crystals. Results : We developed a robust and efficient system for recombinant expression of Pa FabB C161A. Conditions to obtain well diffracting crystals were established. The crystal structure of Pa FabB C161A was solved by molecular replacement at 1.3 Å resolution. Binding site comparison between Pa FabB and Pa FabF revealed a conserved malonyl binding site but differences in the fatty acid binding channel. Conclusions : The Pa FabB C161A crystal structure can be used as a template to facilitate the design of FabB inhibitors.


    Organizational Affiliation

    Department of Biomedicine, University of Bergen, Bergen, 5020, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 1A, B407Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 1 
Gene Names: fabBPA14_43690
EC: 2.3.1.41
UniProt
Find proteins for Q02K94 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02K94 
Go to UniProtKB:  Q02K94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02K94
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
FA [auth B],
GA [auth B],
L [auth A],
M [auth A],
N [auth A],
FA [auth B],
GA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
U [auth A],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
U [auth A],
V [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.228α = 90
b = 102.304β = 90
c = 188.774γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway273588

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.2: 2022-02-16
    Changes: Database references
  • Version 1.3: 2022-02-23
    Changes: Database references