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- PDB-4w82: Enoyl-acyl carrier protein-reductase domain from human fatty acid... -

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Basic information

Entry
Database: PDB / ID: 4w82
TitleEnoyl-acyl carrier protein-reductase domain from human fatty acid synthase
ComponentsFatty acid synthase
KeywordsOXIDOREDUCTASE / fatty acid synthase / fatty acid metabolism / NADPH-dependent / enoyl reductase
Function / homology
Function and homology information


fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development ...fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / : / oleoyl-[acyl-carrier-protein] hydrolase / Fatty acyl-CoA biosynthesis / fatty acyl-[ACP] hydrolase activity / modulation by host of viral process / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / ChREBP activates metabolic gene expression / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / mammary gland development / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / phosphopantetheine binding / monocyte differentiation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / fatty acid biosynthetic process / osteoblast differentiation / melanosome / inflammatory response / cadherin binding / Golgi apparatus / RNA binding / extracellular exosome / 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 synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / 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 / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSippel, K.H. / Vyas, N.K. / Sankaran, B. / Quiocho, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationQ-0581 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of the human Fatty Acid synthase enoyl-acyl carrier protein-reductase domain complexed with triclosan reveals allosteric protein-protein interface inhibition.
Authors: Sippel, K.H. / Vyas, N.K. / Zhang, W. / Sankaran, B. / Quiocho, F.A.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 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 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6636
Polymers73,5562
Non-polymers1074
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-30 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.310, 59.040, 61.430
Angle α, β, γ (deg.)94.960, 101.110, 95.090
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROchain AAA1530 - 18612 - 333
2LEULEUchain BBB1530 - 18652 - 337

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Components

#1: Protein Fatty acid synthase


Mass: 36778.012 Da / Num. of mol.: 2 / Fragment: enoyl-ACP-reductase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASN, FAS / Plasmid: pTYB21 / Cell line (production host): 2566 / Production host: Escherichia coli (E. coli)
References: UniProt: P49327, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis Tris pH 6.5, 100 mM MgCl2, 19% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.7→44.27 Å / Num. obs: 59723 / % possible obs: 93.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.07 / Net I/σ(I): 8.3 / Num. measured all: 231847 / Scaling rejects: 200
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.733.91.2211.21235931470.5490.71193.4
9-44.273.80.0462416094180.9950.02797

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1745)refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vz8

2vz8


Resolution: 1.7→44.267 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 3650 3.08 %Random selection
Rwork0.1867 114986 --
obs0.1877 59723 93.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.57 Å2 / Biso mean: 27.94 Å2 / Biso min: 11.95 Å2
Refinement stepCycle: final / Resolution: 1.7→44.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 4 315 4868
Biso mean--25.74 38.02 -
Num. residues----611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084755
X-RAY DIFFRACTIONf_angle_d1.1176475
X-RAY DIFFRACTIONf_chiral_restr0.042752
X-RAY DIFFRACTIONf_plane_restr0.005824
X-RAY DIFFRACTIONf_dihedral_angle_d12.0691646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3138X-RAY DIFFRACTION5.783TORSIONAL
12B3138X-RAY DIFFRACTION5.783TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72240.32861300.31074398452893
1.7224-1.7460.341240.29384378450292
1.746-1.77090.30361410.29784483462493
1.7709-1.79730.30291340.28434341447592
1.7973-1.82540.32151610.27614379454093
1.8254-1.85540.2551420.27374367450993
1.8554-1.88740.3331460.25974425457193
1.8874-1.92170.30641260.24094465459193
1.9217-1.95860.29861420.22844370451294
1.9586-1.99860.23141380.2144414455293
1.9986-2.04210.23461350.20224456459193
2.0421-2.08960.20021440.18574378452294
2.0896-2.14180.20321340.19114437457193
2.1418-2.19970.20031680.17674413458193
2.1997-2.26450.18261200.16884444456493
2.2645-2.33750.16841430.16224452459594
2.3375-2.42110.2141430.16914378452193
2.4211-2.5180.20721420.16954431457393
2.518-2.63260.24781230.16664433455693
2.6326-2.77140.17121480.16664433458194
2.7714-2.9450.19521530.16174413456694
2.945-3.17230.16761390.16024414455393
3.1723-3.49140.22291330.1594435456893
3.4914-3.99640.17071510.16074301445292
3.9964-5.03390.19261440.16424494463895
5.0339-44.28160.26661460.20984654480098
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)
11.637-0.2895-0.30531.4205-0.30881.47110.0031-0.20920.22950.35240.02130.0751-0.1693-0.044-0.01860.2663-0.00360.03160.2072-0.03140.2266-82.506231.6831-136.3685
20.64520.393-0.17531.2634-0.3340.80590.032-0.02150.00790.0141-0.0182-0.06090.09620.0586-0.00690.15710.0146-0.01780.1642-0.01230.1386-77.977612.0996-140.9482
30.76750.19680.07781.396-0.05461.6356-0.0118-0.1495-0.03890.3286-0.0108-0.11340.1699-0.13920.02090.35580.0274-0.04070.23340.00220.1786-82.34380.58-130.1265
41.3877-0.31660.1262.022-0.01031.38210.05750.0158-0.017-0.0433-0.12920.06890.0575-0.01560.07540.1613-0.01420.01020.16790.00850.1894-80.783521.0367-143.959
51.18560.445-0.45082.3904-0.26691.8132-0.04870.063-0.0731-0.15850.0892-0.06550.1299-0.0969-0.04030.1357-0.0058-0.00350.1671-0.00910.2087-68.7417-20.7017-102.355
60.8797-0.16170.17812.02470.24472.2366-0.05610.0340.1234-0.1689-0.0208-0.0066-0.3296-0.12080.05690.1924-0.0015-0.01520.1750.00870.16-66.10837.5514-106.169
70.63390.08440.30772.2341-1.0281.4262-0.0193-0.0307-0.0723-0.1684-0.0369-0.11970.05760.00450.04260.1431-0.00560.0220.1608-0.0250.1689-65.9223-9.6909-103.6615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1530 through 1611 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1612 through 1711 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1712 through 1804 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1805 through 1861 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1530 through 1648 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1649 through 1769 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1770 through 1865 )B0

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