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- PDB-2ml8: NMR structure of Saccharomyces cerevisiae Acyl Carrier Protein. -

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Basic information

Entry
Database: PDB / ID: 2ml8
TitleNMR structure of Saccharomyces cerevisiae Acyl Carrier Protein.
ComponentsFatty acid synthase subunit alpha
KeywordsTRANSFERASE / ACP / Fatty acid Synthase
Function / homology
Function and homology information


fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / long-chain fatty acid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / long-chain fatty acid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / magnesium ion binding / mitochondrion / cytosol
Similarity search - Function
: / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily ...: / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / 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 / Phosphopantetheine attachment site. / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsWider, G. / Perez, D.R. / Leibundgut, M.
Citation
Journal: To be published
Title: NMR structure of Saccharomyces cerevisiae Acyl Carrier Protein
Authors: Perez, D.R. / Wider, G.
#1: Journal: Biomol.Nmr Assign. / Year: 2009
Title: 1H, 15N, 13C resonance assignment of the acyl carrier protein subunit of the Saccharomyces cerevisiae fatty acid synthase.
Authors: Perez, D.R. / Wider, G.
History
DepositionFeb 20, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid synthase subunit alpha


Theoretical massNumber of molelcules
Total (without water)19,8191
Polymers19,8191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Fatty acid synthase subunit alpha / / Acyl carrier / 3-oxoacyl-[acyl-carrier-protein] reductase / Beta-ketoacyl reductase / 3-oxoacyl- ...Acyl carrier / 3-oxoacyl-[acyl-carrier-protein] reductase / Beta-ketoacyl reductase / 3-oxoacyl-[acyl-carrier-protein] synthase / Beta-ketoacyl synthase


Mass: 19819.492 Da / Num. of mol.: 1 / Fragment: Acyl Carrier, UNP RESIDUES 138-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: FAS2, YPL231W, P1409 / Production host: Escherichia coli (E. coli) / References: UniProt: P19097, fatty-acyl-CoA synthase system

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: 1H, 13C, 15N Resonances Structure of Acyl Carrier Protein of Saccharomyces cerevisiae Fatty acid Synthase
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D HN(CA)CB
1513D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] Acyl Carrier Protein-1, 52 mM KH2PO4 : K2HPO4 (0.685 : 0.315) buffer-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAcyl Carrier Protein-1[U-13C; U-15N]1
52 mMKH2PO4 : K2HPO4 (0.685 : 0.315) buffer-21
Sample conditionsIonic strength: 0.052 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichdata analysis
CYANArefinement
AMBERrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3713 / NOE intraresidue total count: 876 / NOE long range total count: 911 / NOE medium range total count: 931 / NOE sequential total count: 995
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.28 Å / Representative conformer: 1

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