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- PDB-9pqx: Structure of M. tuberculosis type-I FAS in the apo state -

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Basic information

Entry
Database: PDB / ID: 9pqx
TitleStructure of M. tuberculosis type-I FAS in the apo state
Components3-oxoacyl-ACP synthase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid synthase
Function / homology
Function and homology information


fatty acid synthase complex / beta-ketoacyl-[acyl-carrier-protein] synthase I / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid synthase activity / fatty acid biosynthetic process / hydrolase activity
Similarity search - Function
: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / : / : / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain ...: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / : / : / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 3-oxoacyl-ACP synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsMazhab-Jafari, M.T. / Samani, E.K.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)195698 Canada
Canadian Institutes of Health Research (CIHR)419240 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06070 Canada
CitationJournal: Protein Sci / Year: 2026
Title: Structural basis of product recognition by Mycobacterium tuberculosis fatty acid synthase.
Authors: Elnaz Khalili Samani / S M Naimul Hasan / Alexander F A Keszei / Mahtab Heydari / Mohammad T Mazhab-Jafari /
Abstract: Microbial iterative fatty acid synthases (FAS) are versatile multienzymes under scrutiny for their potential as anti-infectious targets and their biotechnological applications. They produce saturated ...Microbial iterative fatty acid synthases (FAS) are versatile multienzymes under scrutiny for their potential as anti-infectious targets and their biotechnological applications. They produce saturated fatty acids with defined chain length and release them as coenzyme A-conjugates. How they recognize appropriate acyl length to initiate the process of product release is unknown. Here, we resolved two intermediate state structures of FAS, one from each of the two organisms: bacterium Mycobacterium tuberculosis and yeast Saccharomyces cerevisiae. These structures reveal how acyl carrier protein (ACP) domain and nascent fatty acids interact with the substrate-promiscuous malonyl-palmitoyl transferase (MPT) domain that is involved in product cleavage from the enzyme. MPT adopts a transient channel necessary for the accommodation of long-chain fatty acids. This channel is formed by the transient retraction of a conserved arginine side chain involved in malonate binding. These insights uncover structural determinants that enable M. tuberculosis type I FAS to produce very long-chain fatty acids used for evading host immunity in tuberculosis (TB).
History
DepositionJul 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
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Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-ACP synthase
B: 3-oxoacyl-ACP synthase
C: 3-oxoacyl-ACP synthase
D: 3-oxoacyl-ACP synthase
E: 3-oxoacyl-ACP synthase
F: 3-oxoacyl-ACP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,962,34712
Polymers1,959,6096
Non-polymers2,7386
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
3-oxoacyl-ACP synthase / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / Fatty acid synthase / Type I polyketide synthase


Mass: 326601.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: kasA_2, A4S10_02647, DKC2_2660, DSJ38_17120, ERS094118_02070, SAMEA2682864_02566
Production host: Escherichia coli (E. coli)
References: UniProt: A0A9P1LAJ1, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Fatty acid synthase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 362078
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113758 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6GJC

6gjc


Accession code: 6GJC / Source name: PDB / Type: experimental model

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