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- PDB-2pff: Structural Insights of Yeast Fatty Acid Synthase -

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Basic information

Entry
Database: PDB / ID: 2pff
TitleStructural Insights of Yeast Fatty Acid Synthase
Components
  • Fatty acid synthase subunit alpha
  • Fatty acid synthase subunit beta
  • Tail protein
KeywordsTRANSFERASE / Fatty acid synthase / acyl-carrier-protein / Beta-ketoacyl reductase / Beta-ketoacyl synthase / dehydratase / Enoyl-[acyl-carrier-protein] reductase / acetyltransferase / malonyltransferase
Function / homology
Function and homology information


: / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / : / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Alpha-Beta Plaits - #2430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1850 / Alpha-Beta Plaits - #10 / Alpha-Beta Plaits / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / : / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi ...Alpha-Beta Plaits - #2430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1850 / Alpha-Beta Plaits - #10 / Alpha-Beta Plaits / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / : / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Other non-globular / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Thiolase-like / Phosphopantetheine attachment site. / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Helix non-globular / Special / Aldolase-type TIM barrel / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsXiong, Y. / Lomakin, I.B. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural Insights of Yeast Fatty Acid Synthase
Authors: Xiong, Y. / Lomakin, I.B. / Steitz, T.A.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE AUTHORS REPORTED THAT THE RESIDUES LABELED UNK IN ALL CHAINS COULD NOT BE ACCURATELY ...SEQUENCE THE AUTHORS REPORTED THAT THE RESIDUES LABELED UNK IN ALL CHAINS COULD NOT BE ACCURATELY MAPPED TO THE AVAIALABLE SEQUENCE DATABASE REFERENCES. NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE PROTEIN IN CHAIN C, F AND I.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit beta
C: Tail protein
D: Fatty acid synthase subunit alpha
E: Fatty acid synthase subunit beta
F: Tail protein
G: Fatty acid synthase subunit alpha
H: Fatty acid synthase subunit beta
I: Tail protein


Theoretical massNumber of molelcules
Total (without water)1,104,5479
Polymers1,104,5479
Non-polymers00
Water00
1
A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit beta
C: Tail protein
D: Fatty acid synthase subunit alpha
E: Fatty acid synthase subunit beta
F: Tail protein
G: Fatty acid synthase subunit alpha
H: Fatty acid synthase subunit beta
I: Tail protein

A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit beta
C: Tail protein
D: Fatty acid synthase subunit alpha
E: Fatty acid synthase subunit beta
F: Tail protein
G: Fatty acid synthase subunit alpha
H: Fatty acid synthase subunit beta
I: Tail protein


Theoretical massNumber of molelcules
Total (without water)2,209,09318
Polymers2,209,09318
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area103160 Å2
ΔGint-597 kcal/mol
Surface area1029670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)231.343, 231.343, 754.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsChains A, B, C, D, E, F and their symmetry mates related by the crystallographic 2-fold.

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Components

#1: Protein Fatty acid synthase subunit alpha / Includes: Acyl carrier / 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) (Beta-ketoacyl ...Includes: Acyl carrier / 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) (Beta-ketoacyl reductase) / 3-oxoacyl-[acyl-carrier-protein] synthase (EC 2.3.1.41) (Beta-ketoacyl synthase)


Mass: 171121.531 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: YIT613 / References: UniProt: P19097, fatty-acyl-CoA synthase system
#2: Protein Fatty acid synthase subunit beta / Includes: 3- hydroxypalmitoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.61) / Enoyl-[acyl- ...Includes: 3- hydroxypalmitoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.61) / Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) / [Acyl- carrier-protein] acetyltransferase (EC 2.3.1.38) / [Acyl-carrier- protein] malonyltransferase (EC 2.3.1.39) / S-acyl fatty acid synthase thioesterase (EC 3.1.2.14)


Mass: 191510.812 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: YIT613 / References: UniProt: P07149, fatty-acyl-CoA synthase system
#3: Protein Tail protein


Mass: 5549.833 Da / Num. of mol.: 3 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7 microleter samle and 3 microleter buffer: 15% PEG3350, 20mM HEPES (pH7.5), 3mM Mg acetate, 0.3M KCl, 30mM Ca cloride, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
1,2,3,41
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 8.2.21
SYNCHROTRONAPS 24-ID-C2
SYNCHROTRONNSLS X253
SYNCHROTRONCHESS A14
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4→60 Å / Num. all: 172942 / Num. obs: 170640 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 140 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 10
Reflection shellResolution: 4→4.1 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CDH

2cdh


Resolution: 4→60 Å / Isotropic thermal model: Isotropic / Cross valid method: throuout / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was solved using 2 data sets (space group P43212 and P21). Both these data sets are included in the sf file. About 50% of the residues were built and refined as poly-alanine. ...Details: The structure was solved using 2 data sets (space group P43212 and P21). Both these data sets are included in the sf file. About 50% of the residues were built and refined as poly-alanine. Additional residues were seen in the electron density (chains C, F, I) that could not be mapped to the available sequence. The authors reported the residues modeled as poly-alanine as UNK since their register against the available sequence database references was uncertain.
RfactorNum. reflection% reflectionSelection details
Rfree0.346 8382 -random
Rwork0.319 ---
all-172942 --
obs-170640 98.7 %-
Displacement parametersBiso mean: 150 Å2
Refinement stepCycle: LAST / Resolution: 4→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms71862 0 0 0 71862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.89

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