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- PDB-3hmj: Saccharomyces cerevisiae FAS type I -

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Basic information

Entry
Database: PDB / ID: 3hmj
TitleSaccharomyces cerevisiae FAS type I
Components
  • Fatty acid synthase subunit alpha
  • Fatty acid synthase subunit beta
KeywordsTRANSFERASE / FAS / PPT / phosphopantetheine transferase / fatty acid / multienyzme / Fatty acid biosynthesis / Lipid synthesis / Multifunctional enzyme / NAD / NADP / Oxidoreductase / Phosphoprotein / Hydrolase / Lyase
Function / homology
Function and homology information


fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity ...fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / long-chain fatty acid biosynthetic process / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #120 / Transcription Elongation Factor S-II; Chain A - #70 / Lipocalin - #700 / Arylsulfatase, C-terminal domain - #100 / Alpha-Beta Plaits - #3320 / Alpha-Beta Plaits - #3330 / Helix Hairpins - #1400 / Hydrophobic Seed Protein / Hydrophobic Seed Protein - #10 / UDP-galactose 4-epimerase; domain 1 - #70 ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #120 / Transcription Elongation Factor S-II; Chain A - #70 / Lipocalin - #700 / Arylsulfatase, C-terminal domain - #100 / Alpha-Beta Plaits - #3320 / Alpha-Beta Plaits - #3330 / Helix Hairpins - #1400 / Hydrophobic Seed Protein / Hydrophobic Seed Protein - #10 / UDP-galactose 4-epimerase; domain 1 - #70 / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / 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 subunit beta, insertion 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 subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / 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 / FAS1-like, dehydratase domain region / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / Arylsulfatase, C-terminal domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Transcription Elongation Factor S-II; Chain A / UDP-galactose 4-epimerase; domain 1 / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Helix Hairpins / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Thiolase-like / Phosphopantetheine attachment site. / Helix non-globular / Lipocalin / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Special / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CER / FLAVIN MONONUCLEOTIDE / 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
AuthorsJohansson, P. / Mulinacci, B. / Koestler, C. / Vollrath, R. / Oesterhelt, D. / Grininger, M.
CitationJournal: Structure / Year: 2009
Title: Multimeric options for the auto-activation of the Saccharomyces cerevisiae FAS type I megasynthase
Authors: Johansson, P. / Mulinacci, B. / Koestler, C. / Vollrath, R. / Oesterhelt, D. / Grininger, M.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit alpha
C: Fatty acid synthase subunit alpha
G: Fatty acid synthase subunit beta
H: Fatty acid synthase subunit beta
I: Fatty acid synthase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,310,41912
Polymers1,308,3746
Non-polymers2,0456
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46160 Å2
ΔGint-247 kcal/mol
Surface area483830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.884, 231.884, 756.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A, 1748-1766
211CHAIN B, 1748-1766
311CHAIN C, 1748-1766
112CHAIN A, 1768-1886
212CHAIN B, 1768-1886
312CHAIN C, 1768-1886

NCS ensembles :
ID
1
2

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Components

#1: Protein Fatty acid synthase subunit alpha


Mass: 207184.422 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FAS2 / References: UniProt: P19097, fatty-acyl-CoA synthase system
#2: Protein Fatty acid synthase subunit beta


Mass: 228940.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FAS1 / References: UniProt: P07149, fatty-acyl-CoA synthase system
#3: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN


Mass: 225.284 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antibiotic*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.039 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 4→25 Å / Num. all: 169821 / Num. obs: 168120 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 4→4.3 Å / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
Cootmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VKZ

2vkz


Resolution: 4→19.999 Å / SU ML: 0.64 / σ(F): 1.34 / Stereochemistry target values: ML
Details: The high-resolution PPT domain (pdb-id 2WAS) was placed by rigid body refinement using the low-resolution data of the full FAS complex (pdb-id 2VKZ)
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 8521 5.07 %Thin shells
Rwork0.2662 ---
obs0.2662 168120 97.34 %-
all-169639 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.917 Å2 / ksol: 0.263 e/Å3
Refinement stepCycle: LAST / Resolution: 4→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms88701 0 129 0 88830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188850
X-RAY DIFFRACTIONf_angle_d1.167119437
X-RAY DIFFRACTIONf_dihedral_angle_d18.58132331
X-RAY DIFFRACTIONf_chiral_restr0.07113368
X-RAY DIFFRACTIONf_plane_restr0.00415376
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A19X-RAY DIFFRACTIONPOSITIONAL
12B19X-RAY DIFFRACTIONPOSITIONAL0.009
13C51X-RAY DIFFRACTIONPOSITIONAL0.012
21A875X-RAY DIFFRACTIONPOSITIONAL
22B875X-RAY DIFFRACTIONPOSITIONAL0
23C875X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.04510.38032540.38135231X-RAY DIFFRACTION97.46
4.0451-4.09230.38632470.37145317X-RAY DIFFRACTION97.89
4.0923-4.14180.34992850.36235348X-RAY DIFFRACTION98.46
4.1418-4.19370.38862870.35735263X-RAY DIFFRACTION98.4
4.1937-4.24840.31763200.34835299X-RAY DIFFRACTION98.23
4.2484-4.3060.33082930.3325297X-RAY DIFFRACTION98.29
4.306-4.36690.31962800.32485314X-RAY DIFFRACTION98.26
4.3669-4.43140.33093050.31765290X-RAY DIFFRACTION97.9
4.4314-4.49990.3222450.3115327X-RAY DIFFRACTION98.34
4.4999-4.57280.30132910.30245312X-RAY DIFFRACTION98.11
4.5728-4.65070.30272740.29325341X-RAY DIFFRACTION98.3
4.6507-4.73410.30193030.29045315X-RAY DIFFRACTION98.15
4.7341-4.82390.28262920.28795317X-RAY DIFFRACTION97.89
4.8239-4.9210.28252640.28515328X-RAY DIFFRACTION98.29
4.921-5.02630.27582880.27955327X-RAY DIFFRACTION98.25
5.0263-5.14130.28652700.28065379X-RAY DIFFRACTION98.02
5.1413-5.26760.27442760.26875338X-RAY DIFFRACTION98.27
5.2676-5.40730.25852880.26995323X-RAY DIFFRACTION97.87
5.4073-5.56310.26253210.2685285X-RAY DIFFRACTION97.78
5.5631-5.73860.26062810.27385339X-RAY DIFFRACTION97.89
5.7386-5.93850.26022850.26525364X-RAY DIFFRACTION97.6
5.9385-6.16960.25032790.25985315X-RAY DIFFRACTION97.27
6.1696-6.44140.25123310.25185289X-RAY DIFFRACTION96.86
6.4414-6.76850.21892790.23995309X-RAY DIFFRACTION96.96
6.7685-7.17410.23412580.23415354X-RAY DIFFRACTION96.44
7.1741-7.69850.21192620.23085367X-RAY DIFFRACTION96.59
7.6985-8.42030.20092690.19875344X-RAY DIFFRACTION95.56
8.4203-9.52180.15962980.17735299X-RAY DIFFRACTION95.3
9.5218-11.59380.18123040.17035306X-RAY DIFFRACTION93.86
11.5938-19.99910.28242920.24945362X-RAY DIFFRACTION92.45
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.02860.06460.06440.0024-0.0213-0.2984-1.3386-1.5318-0.97530.66250.27850.7317-1.16121.648203.5126-0.62640.4132.1502-0.00843.2165214.441196.0183-70.7788
2-0.3265-0.106-0.057-0.68940.6837-0.1961.84940.65050.87190.2882-1.9467-0.36730.4118-0.8673-02.4638-0.64240.09592.35340.65414.198
30.0048-0.07080.0658-0.00780.0503-0.0139-0.1027-1.9905-0.60510.1436-0.77671.3108-1.29673.6364-03.2492-0.4914-0.49882.2455-0.30912.8033
4-0.3780.732-0.9928-0.6827-1.17550.38450.17151.2611-2.40841.0474-0.25080.4789-0.2498-0.582202.188-0.2175-0.63553.0359-0.40362.2826
5-0.04090.00590.0214-0.1117-0.0727-0.0017-1.1303-2.0428-1.1119-1.1208-0.0674-0.619-0.18710.7361-03.11850.619-0.04923.51870.7143.2025
6-0.97560.3762-0.4051-0.6473-0.9337-1.4853-0.94770.37891.03130.4506-2.76652.02182.1324-1.249703.73020.0258-0.06034.28980.69894.2184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A, 1748-1766
2X-RAY DIFFRACTION2chain A, 1768-1886
3X-RAY DIFFRACTION3chain B, 1748-1766
4X-RAY DIFFRACTION4chain B, 1768-1886
5X-RAY DIFFRACTION5chain C, 1748-1766
6X-RAY DIFFRACTION6chain C, 1768-1886

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