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- PDB-2uv8: Crystal structure of yeast fatty acid synthase with stalled acyl ... -

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Basic information

Entry
Database: PDB / ID: 2uv8
TitleCrystal structure of yeast fatty acid synthase with stalled acyl carrier protein at 3.1 angstrom resolution
Components
  • FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
  • FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
KeywordsTRANSFERASE / FATTY ACID BIOSYNTHESIS / MALONYL/PALMITOYL TRANSFERASE / PHOSPHOPANTETHEINE / FATTY ACID SYNTHASE / OXIDOREDUCTASE / LIPID SYNTHESIS / SUBSTRATE SHUTTLING / ACYL CARRIER PROTEIN / KETOACYL REDUCTASE / ACETYL TRANSFERASE / ENOYL REDUCTASE / PHOSPHORYLATION / KETOACYL SYNTHASE / FATTY ACID SYNTHESIS / MULTIFUNCTIONAL ENZYME / NAD / NADP / LYASE / YEAST / HYDROLASE / DEHYDRATASE
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
Alpha-Beta Plaits - #2490 / Helix Hairpins - #1410 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / 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 ...Alpha-Beta Plaits - #2490 / Helix Hairpins - #1410 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
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: 3.1 Å
AuthorsLeibundgut, M. / Jenni, S. / Frick, C. / Ban, N.
CitationJournal: Science / Year: 2007
Title: Structural Basis for Substrate Delivery by Acyl Carrier Protein in the Yeast Fatty Acid Synthase
Authors: Leibundgut, M. / Jenni, S. / Frick, C. / Ban, N.
History
DepositionMar 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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 (FAS2)
B: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
C: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
G: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
H: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
I: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,310,3719
Polymers1,309,0026
Non-polymers1,3693
Water00
1
A: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
B: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
C: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
G: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
H: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
I: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
hetero molecules

A: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
B: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
C: FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2)
G: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
H: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
I: FATTY ACID SYNTHASE SUBUNIT BETA (FAS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,620,74218
Polymers2,618,00412
Non-polymers2,7386
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)230.600, 230.600, 784.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FATTY ACID SYNTHASE SUBUNIT ALPHA (FAS2) / FATTY ACID SYNTHASE


Mass: 207393.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: PHOSPHOPANTETHEINE PROSTHETIC GROUP COVALENTLY LINKED TO SERINE 180 OF CHAIN A, B, C
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P19097, fatty-acyl-CoA synthase system
#2: Protein FATTY ACID SYNTHASE SUBUNIT BETA (FAS1) / FATTY ACID SYNTHASE


Mass: 228940.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P07149, fatty-acyl-CoA synthase system
#3: 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: 4.33 Å3/Da / Density % sol: 71.38 %
Crystal growpH: 7.1 / Details: pH 7.10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.1→12 Å / Num. obs: 341077 / % possible obs: 89.7 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 73.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.9
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2UVB AND 2UVC

2uvb
PDB Unreleased entry

2uvc
PDB Unreleased entry


Resolution: 3.1→12 Å
RfactorNum. reflection% reflection
Rfree0.25 13730 4 %
Rwork0.2 --
obs-327347 86.1 %
Displacement parametersBiso mean: 72.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms85869 0 93 0 85962

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