8Z5F

Crystal structure of beta-ketoacyl-ACP synthase FabF K336A in complex with decanoyl-ACP from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.424 

Starting Model: experimental
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Literature

The beta-Ketoacyl-ACP Synthase FabF Catalyzes Carbon-Carbon Bond Formation in a Bimodal Pattern for Fatty Acid Biosynthesis.

Zhang, L.Huang, Y.Wang, Y.Cai, C.Zhang, L.Ye, F.

(2024) Angew Chem Int Ed Engl : e202407921-e202407921

  • DOI: https://doi.org/10.1002/anie.202407921
  • Primary Citation of Related Structures:  
    8Z5C, 8Z5D, 8Z5E, 8Z5F

  • PubMed Abstract: 

    Fatty acids produced by the type-II fatty acid biosynthesis pathway (FAS-II) are essential biomaterials for bacterial membrane construction and numerous metabolic routes. The β-ketoacyl-ACP synthase FabF catalyzes the key C-C bond formation step for fatty acid extension in FAS-II. Here, we revealed the substrate recognition and catalytic mechanisms of FabF by determining FabF-ACP complexes. FabF displays a distinctive bimodal catalytic pattern specifically on C6 and C10 acyl-ACP substrates. It utilizes positively charged residues located on the η3-helix and loop1 regions near the catalytic tunnel entrance to bind ACP, and two hydrophobic cavities as well as "front", "middle", and "back" door residues to specifically stabilize C6 and C10 acyl substrates for preferential catalysis. Further quantum chemistry calculations suggest that the FabF catalytic residues Lys336 and His304 facilitate proton transfer during condensation catalysis and C-C bond formation. Our results provide key mechanistic insights into the biosynthesis of molecular carbon skeletons based on ketosynthases that are highly conserved through the FAS and polyketide synthase (PKS) analogous biosynthetic routes, broaden the understanding of the tricarboxylic acid cycle that utilizes lipoic acid derived from C8-ACP accumulated due to the FabF distinctive catalytic pattern for oxidative decarboxylations, and may facilitate the development of narrow-spectrum antibacterial drugs.


  • Organizational Affiliation

    Shanghai Jiao Tong University School of Medicine, Pharmacology and chemical biology, Building #3, Room #213,, No.280 South Chongqing Road, 200025, Shanghai, CHINA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 2
A, B
412Helicobacter pyloriMutation(s): 1 
Gene Names: CV729_03800DD764_02895EC543_05795
EC: 2.3.1.179
UniProt
Find proteins for A0A438WLJ1 (Helicobacter pylori)
Explore A0A438WLJ1 
Go to UniProtKB:  A0A438WLJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A438WLJ1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein
C, D
86Helicobacter pyloriMutation(s): 0 
Gene Names: 
acpPacpP_2AA971_03770ACM26_04180ACM37_01955AEY53_01410AM496_03540AM497_00990AP069_0203010AV920_0203940B0X29_03800B0X45_00570B0X60_00365BB384_06970BB395_06520BB411_01045BB413_00115BB414_01745BB424_04705BB425_06615BB461_04255BB464_01665BGL66_01950BGL69_04330BGL75_08125BHU51_05610BV499_06310BZK21_01490BZK27_00480C2R62_01950C2R66_01755C2R85_07050C2R93_06190C2R96_08170C2S01_06755C2S04_07420C2S07_01945C2S19_07900C2S39_07050C2S42_07730C2S44_03705CGC32_03355CHC155_06320CV726_04705CV727_03490CV728_03285CV729_03805CV730_03675D2C82_03205D2C84_02485D8X56_02965DD750_02355DD779_02830DDP35_03120DDP37_03425DDP42_02985DDP44_02790DDP47_01920DDP49_02455DDP57_02830EC503_03190EC505_03755EC511_02300EC517_03570EC518_00005EC525_03720EC532_06155EC533_02570EC547_02800EC550_02360EC556_02625EC558_03510EC565_04600EC572_05195EC585_03955EC589_03210EC590_01945ECC07_01920ECC12_02075ECC24_01300ECC33_03205ECC34_03320ECC35_03300ECC38_04160ECC40_02350ECC41_02110ECC43_03930ECC49_04200EDA74_03725EDB75_01310EDC13_02400EGV97_06255EGW01_07925EPC79_07230EPC80_01035F7187_05530F7189_04775F7197_04985F7198_04545F7213_06745F7220_05045F7229_06460HPF17_0447HPF209_0807HPF210_0847HPF72_0568HPK21_01210HPMKM5_0823HPPMSS1_c00678HPY1846_06495

UniProt
Find proteins for Q5EDC8 (Helicobacter pylori)
Explore Q5EDC8 
Go to UniProtKB:  Q5EDC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EDC8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.424 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.312α = 90
b = 153.586β = 113.28
c = 72.442γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22077081

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release