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- PDB-2vcy: Crystal Structure of 2-Enoyl Thioester Reductase of Human FAS II -

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Basic information

Entry
Database: PDB / ID: 2vcy
TitleCrystal Structure of 2-Enoyl Thioester Reductase of Human FAS II
ComponentsTRANS-2-ENOYL-COA REDUCTASE
KeywordsOXIDOREDUCTASE / NADP / POLYMORPHISM / MITOCHONDRION / FATTY ACID BIOSYNTHESIS / ENOYL THIOESTER REDUCTASE / LIPID SYNTHESIS / TRANSIT PEPTIDE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) / trans-2-enoyl-CoA reductase (NADPH) activity / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion / nucleus
Similarity search - Function
Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enoyl-[acyl-carrier-protein] reductase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsHaapalainen, A.M. / Pudas, R. / Smart, O.S. / Wierenga, R.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Enzymological Studies of 2-Enoyl Thioester Reductase of the Human Mitochondrial Fas II Pathway: New Insights Into its Substrate Recognition Properties.
Authors: Chen, Z.J. / Pudas, R. / Sharma, S. / Smart, O.S. / Juffer, A.H. / Hiltunen, J.K. / Wierenga, R.K. / Haapalainen, A.M.
History
DepositionSep 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANS-2-ENOYL-COA REDUCTASE
B: TRANS-2-ENOYL-COA REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,50013
Polymers74,4442
Non-polymers1,05711
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-22.6 kcal/mol
Surface area35130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.620, 104.620, 146.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1475, 0.98019, 0.13221), (0.98673, 0.13666, 0.08772), (0.06791, 0.1434, -0.98733)-53.60578, 47.96128, -12.56546
2given(-0.1475, 0.98673, 0.06791), (0.98019, 0.13666, 0.1434), (0.13221, 0.08772, -0.98733)-54.3784, 47.79124, -9.52591

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Components

#1: Protein TRANS-2-ENOYL-COA REDUCTASE / HSNRBF-1 / NRBF-1


Mass: 37221.859 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BV79, trans-2-enoyl-CoA reductase (NADPH)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT DOES NOT CONTAIN MITOCHONDRIAL SIGNAL AND STARTS FROM RESIDUE ALA31.

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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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growpH: 8.5 / Details: 2M AMMONIUM SULFATE, 100 MM TRIS HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9421
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2005 / Details: MIRRORS
RadiationMonochromator: FIXED WITH DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9421 Å / Relative weight: 1
ReflectionResolution: 2.41→33.79 Å / Num. obs: 32130 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.7
Reflection shellResolution: 2.41→2.54 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUF

1guf


Resolution: 2.41→33.79 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: RESIDUES 31-41 ARE NOT PRESENT IN THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 1391 5.1 %RANDOM
Rwork0.2071 ---
obs0.2101 27176 84.43 %-
Refinement stepCycle: LAST / Resolution: 2.41→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 55 290 5401

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