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- PDB-8zev: Crystal structure of the dehydratase domain of human fatty acid s... -

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Basic information

Entry
Database: PDB / ID: 8zev
TitleCrystal structure of the dehydratase domain of human fatty acid synthase
ComponentsFatty acid synthase
KeywordsBIOSYNTHETIC PROTEIN / Human / Fatty acid synthase / FASN / Dehydratase domain / DH
Function / homology
Function and homology information


fatty-acid synthase system / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / fatty-acyl-CoA biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / glycogen granule ...fatty-acid synthase system / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / fatty-acyl-CoA biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / glycogen granule / oleoyl-[acyl-carrier-protein] hydrolase / Fatty acyl-CoA biosynthesis / fatty acyl-[ACP] hydrolase activity / host-mediated perturbation of viral process / ChREBP activates metabolic gene expression / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / [acyl-carrier-protein] S-malonyltransferase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / acetyl-CoA metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / mammary gland development / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / monocyte differentiation / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to nutrient / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / fatty acid biosynthetic process / osteoblast differentiation / melanosome / cadherin binding / inflammatory response / Golgi apparatus / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...: / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
IODIDE ION / Fatty acid synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Chembiochem / Year: 2024
Title: Structural Basis of the Dehydratase Module (hDH) of Human Fatty Acid Synthase.
Authors: Cai, C. / Huang, Y. / Zhang, L. / Zhang, L.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid synthase
B: Fatty acid synthase
C: Fatty acid synthase
D: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,27511
Polymers112,3874
Non-polymers8887
Water13,457747
1
A: Fatty acid synthase
hetero molecules

B: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7016
Polymers56,1932
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+1/31
Buried area2790 Å2
ΔGint-4 kcal/mol
Surface area22800 Å2
MethodPISA
2
C: Fatty acid synthase
D: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5745
Polymers56,1932
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-4 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.130, 108.130, 221.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Fatty acid synthase / Type I fatty acid synthase


Mass: 28096.709 Da / Num. of mol.: 4 / Fragment: dehydratase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASN, FAS / Production host: Escherichia coli (E. coli)
References: UniProt: P49327, fatty-acid synthase system, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, 3- ...References: UniProt: P49327, fatty-acid synthase system, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, 3-oxoacyl-[acyl-carrier-protein] reductase, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific), oleoyl-[acyl-carrier-protein] hydrolase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 mM Imidazole, pH 6.5, 10 mM Sodium Iodide, and 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→35.39 Å / Num. obs: 139108 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.019 / Rrim(I) all: 0.086 / Χ2: 0.98 / Net I/σ(I): 20.4 / Num. measured all: 2760557
Reflection shellResolution: 1.8→1.85 Å / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 1.594 / Num. measured all: 183066 / Num. unique obs: 10137 / CC1/2: 0.741 / Rpim(I) all: 0.385 / Rrim(I) all: 1.64 / Χ2: 0.85 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.21 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 7117 5.12 %
Rwork0.2072 --
obs0.2083 139013 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→31.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7717 0 7 747 8471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097953
X-RAY DIFFRACTIONf_angle_d1.25210853
X-RAY DIFFRACTIONf_dihedral_angle_d14.7192850
X-RAY DIFFRACTIONf_chiral_restr0.081237
X-RAY DIFFRACTIONf_plane_restr0.0161386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.30642390.28754305X-RAY DIFFRACTION100
1.82-1.840.3352300.28254320X-RAY DIFFRACTION100
1.84-1.860.3082740.28194362X-RAY DIFFRACTION100
1.86-1.890.30772130.27274298X-RAY DIFFRACTION100
1.89-1.910.33922460.30464354X-RAY DIFFRACTION100
1.91-1.940.31572600.28494348X-RAY DIFFRACTION100
1.94-1.970.29312470.27464373X-RAY DIFFRACTION100
1.97-20.30372410.26094333X-RAY DIFFRACTION100
2-2.030.2652440.24864328X-RAY DIFFRACTION100
2.03-2.060.27941960.24694372X-RAY DIFFRACTION100
2.06-2.10.2542020.24414409X-RAY DIFFRACTION100
2.1-2.130.26042200.24344418X-RAY DIFFRACTION100
2.13-2.180.26252650.23524317X-RAY DIFFRACTION100
2.18-2.220.2722680.23544348X-RAY DIFFRACTION100
2.22-2.270.27322400.23554347X-RAY DIFFRACTION100
2.27-2.320.22312490.22314372X-RAY DIFFRACTION100
2.32-2.380.23722100.22854413X-RAY DIFFRACTION100
2.38-2.440.27192350.23264386X-RAY DIFFRACTION100
2.44-2.510.25332280.22964423X-RAY DIFFRACTION100
2.51-2.60.25252420.22324366X-RAY DIFFRACTION100
2.6-2.690.25682380.22034382X-RAY DIFFRACTION100
2.69-2.80.24631980.21754437X-RAY DIFFRACTION100
2.8-2.920.22811950.21964481X-RAY DIFFRACTION100
2.92-3.080.22672260.2084408X-RAY DIFFRACTION100
3.08-3.270.22542660.21074399X-RAY DIFFRACTION100
3.27-3.520.22562640.18944417X-RAY DIFFRACTION100
3.52-3.880.18672620.18154430X-RAY DIFFRACTION100
3.88-4.430.19992560.16654462X-RAY DIFFRACTION100
4.44-5.580.17742260.16644560X-RAY DIFFRACTION100
5.58-31.210.21212370.20854728X-RAY DIFFRACTION100

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