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- PDB-8g7x: Human fatty acid synthase dehydratase domain -

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Basic information

Entry
Database: PDB / ID: 8g7x
TitleHuman fatty acid synthase dehydratase domain
Components3-hydroxyacyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / Human / fatty acid synthase / dehydratase
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 / glycogen granule / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity ...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 / glycogen granule / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / Fatty acyl-CoA biosynthesis / host-mediated perturbation of viral process / ChREBP activates metabolic gene expression / 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 / acetyl-CoA metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / mammary gland development / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase 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 / osteoblast differentiation / fatty acid biosynthetic process / melanosome / cadherin binding / inflammatory response / Golgi apparatus / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide synthase dehydratase / : / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : ...Polyketide synthase dehydratase / : / 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 / Thiol Ester Dehydrase; Chain A / 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 / PKS_KR / Beta-ketoacyl synthase / 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 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / THIOCYANATE ION / Fatty acid synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.815 Å
AuthorsAkey, D.L. / Konwerski, J.R. / McCullough, T.M. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK042303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM138396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118101 United States
CitationJournal: Structure / Year: 2023
Title: Structure of a modular polyketide synthase reducing region.
Authors: McCullough, T.M. / Dhar, A. / Akey, D.L. / Konwerski, J.R. / Sherman, D.H. / Smith, J.L.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,79012
Polymers55,1682
Non-polymers62210
Water6,539363
1
A: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0318
Polymers27,5841
Non-polymers4477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7594
Polymers27,5841
Non-polymers1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.407, 70.409, 78.371
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / Type I fatty acid synthase


Mass: 27584.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASN, FAS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P49327, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 13% PEG 3350, 200 mM sodium thiocyanate / PH range: 6.9-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40862 / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3 / Num. unique obs: 8460 / % possible all: 81.5

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.15.2-3472refinement
REFMAC5refinement
MOLREPphasing
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.815→37.855 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 2072 5.08 %
Rwork0.1679 --
obs0.1698 40777 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.815→37.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 33 363 4116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083920
X-RAY DIFFRACTIONf_angle_d0.9285339
X-RAY DIFFRACTIONf_dihedral_angle_d17.5082298
X-RAY DIFFRACTIONf_chiral_restr0.065605
X-RAY DIFFRACTIONf_plane_restr0.007686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8153-1.85750.25331010.22921824X-RAY DIFFRACTION69
1.8575-1.9040.28761150.20472287X-RAY DIFFRACTION86
1.904-1.95550.23721370.18272533X-RAY DIFFRACTION95
1.9555-2.0130.22861540.17422656X-RAY DIFFRACTION100
2.013-2.0780.20061450.16482646X-RAY DIFFRACTION100
2.078-2.15230.2211470.1622643X-RAY DIFFRACTION100
2.1523-2.23840.2211380.16652657X-RAY DIFFRACTION100
2.2384-2.34030.2291380.16622687X-RAY DIFFRACTION100
2.3403-2.46360.20991400.16572670X-RAY DIFFRACTION100
2.4636-2.6180.22431490.17832649X-RAY DIFFRACTION100
2.618-2.820.23091360.18352668X-RAY DIFFRACTION100
2.82-3.10370.21611390.17032674X-RAY DIFFRACTION100
3.1037-3.55250.19291330.17062693X-RAY DIFFRACTION100
3.5525-4.47470.17791400.14592694X-RAY DIFFRACTION100
4.4747-37.8550.17371600.16572724X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.0742-0.2614-0.09020.89930.16861.24630.0201-0.0791-0.00460.0069-0.0093-0.0575-0.05760.1059-0.00240.1118-0.0041-0.01480.1095-0.00780.11295.7402-17.222629.9254
20.1635-0.2688-0.07341.3568-0.10511.80550.048-0.25-0.06990.12260.0198-0.00270.02430.0886-0.06180.124-0.0008-0.00930.10290.01030.11944.7302-19.873337.82
32.26940.6384-0.19651.4436-0.05031.6088-0.09070.08420.3468-0.10630.04210.1373-0.2990.04130.03180.18560.0025-0.02080.11440.02310.1703-3.439-2.03622.6499
41.88240.23040.11240.838-0.1750.6909-0.00150.03190.2559-0.05990.00570.0415-0.2155-0.03270.04150.11520.02450.01480.0574-0.00650.1318-6.3608-5.690428.4496
51.2920.2193-0.0160.87250.02551.50240.04050.1556-0.0448-0.04670.0087-0.06420.11610.0744-0.04420.13980.0073-0.00160.1406-0.01130.14388.5189-31.238514.5613
61.94660.1766-0.06341.48610.221.51060.11020.18670.1574-0.1749-0.0339-0.16830.01240.0236-0.09740.16040.02360.03520.22330.01370.129812.5435-28.82747.5866
71.50340.3715-0.07662.3955-0.16691.89860.03390.1017-0.31640.0209-0.02730.15890.3093-0.4185-0.04270.1691-0.0673-0.00290.2065-0.03330.1897-5.4122-43.350715.7643
81.9510.2819-0.72811.2150.152.1311-0.04250.3503-0.1438-0.0138-0.0310.00970.4144-0.4366-0.00620.2122-0.045-0.02560.224-0.08390.1392-4.5719-39.28448.6253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 856:923)
2X-RAY DIFFRACTION2(chain A and resseq 924:964)
3X-RAY DIFFRACTION3(chain A and resseq 965:1041)
4X-RAY DIFFRACTION4(chain A and resseq 1042:1103)
5X-RAY DIFFRACTION5(chain B and resseq 857:923)
6X-RAY DIFFRACTION6(chain B and resseq 924:964)
7X-RAY DIFFRACTION7(chain B and resseq 965:1041)
8X-RAY DIFFRACTION8(chain B and resseq 1042:1102)

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