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- PDB-8uy1: Methylenetetrahydrofolate reductase from Chaetomium thermophilum ... -

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Basic information

Entry
Database: PDB / ID: 8uy1
TitleMethylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State
ComponentsMethylenetetrahydrofolate reductase-like protein
KeywordsOXIDOREDUCTASE / methylenetetrahydrofolate reductase / NADPH activity / oxidoreductase activity / acting on the CH-NH group of donors / NAD or NADP as acceptor cobalamin binding / one-carbon metabolism
Function / homology
Function and homology information


methylenetetrahydrofolate reductase [NAD(P)H] activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function
Eukaryotic-type methylenetetrahydrofolate reductase / : / MTHFR, SAM-binding regulatory domain / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / FAD-linked oxidoreductase-like
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Methylenetetrahydrofolate reductase-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsYamada, K. / Mendoza, J. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1945174 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of S-adenosylmethionine-dependent allosteric transition from active to inactive states in methylenetetrahydrofolate reductase.
Authors: Yamada, K. / Mendoza, J. / Koutmos, M.
History
DepositionNov 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Methylenetetrahydrofolate reductase-like protein
A: Methylenetetrahydrofolate reductase-like protein
B: Methylenetetrahydrofolate reductase-like protein
C: Methylenetetrahydrofolate reductase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,7738
Polymers281,6314
Non-polymers3,1424
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.972, 151.380, 188.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Methylenetetrahydrofolate reductase-like protein


Mass: 70407.742 Da / Num. of mol.: 4 / Mutation: E21Q,L393M,V516F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033700 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5U9
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1-1 ratio protein to reservoir solution Protein: 25 mM Tris, pH 7.4, 50 mM potassium chloride, 500 uM FAD, and 1 mM TCEP Reservoir Solution: 0.1 M HEPES, pH 7.5, 0.1 mM potassium chloride, ...Details: 1-1 ratio protein to reservoir solution Protein: 25 mM Tris, pH 7.4, 50 mM potassium chloride, 500 uM FAD, and 1 mM TCEP Reservoir Solution: 0.1 M HEPES, pH 7.5, 0.1 mM potassium chloride, 20 mM magnesium chloride, 22% poly(acrylic acid sodium salt) 5,100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.41→52.04 Å / Num. obs: 46407 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.067 / Rrim(I) all: 0.177 / Χ2: 0.92 / Net I/σ(I): 7.7
Reflection shellResolution: 3.41→3.53 Å / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 2.805 / Num. measured all: 32082 / Num. unique obs: 4499 / CC1/2: 0.466 / Rpim(I) all: 1.122 / Rrim(I) all: 3.024 / Χ2: 0.82 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
DIALSdata reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→52.04 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.914 / SU B: 82.341 / SU ML: 0.527 / Cross valid method: THROUGHOUT / ESU R Free: 0.623 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25564 2181 5 %RANDOM
Rwork0.21556 ---
obs0.21759 41089 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 157.458 Å2
Baniso -1Baniso -2Baniso -3
1-7.35 Å20 Å2-0 Å2
2---3.86 Å20 Å2
3----3.49 Å2
Refinement stepCycle: 1 / Resolution: 3.49→52.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19085 0 212 4 19301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01219811
X-RAY DIFFRACTIONr_bond_other_d0.0080.01618293
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.83826891
X-RAY DIFFRACTIONr_angle_other_deg1.3821.7842105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28652355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.6095160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56103309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.22790
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0223838
X-RAY DIFFRACTIONr_gen_planes_other0.0090.024760
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.92910.6199444
X-RAY DIFFRACTIONr_mcbond_other6.92910.6199444
X-RAY DIFFRACTIONr_mcangle_it10.92119.11211791
X-RAY DIFFRACTIONr_mcangle_other10.92119.11211792
X-RAY DIFFRACTIONr_scbond_it6.70610.96110367
X-RAY DIFFRACTIONr_scbond_other6.70510.96110364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.87520.00815101
X-RAY DIFFRACTIONr_long_range_B_refined17.568135.0390900
X-RAY DIFFRACTIONr_long_range_B_other17.568135.0390901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.49→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 163 -
Rwork0.346 3001 -
obs--99.84 %
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)
12.69280.50071.58592.00730.7462.48150.178-0.5941-0.40730.1659-0.21720.30580.1363-0.46940.03920.0912-0.05410.00120.18740.10090.208823.218918.508836.7847
22.24250.4034-0.47252.91450.50033.36820.0606-0.5770.3361-0.09060.0519-0.544-0.75710.5805-0.11250.183-0.1575-0.02450.34120.01110.294364.700542.96313.0952
32.05910.08290.54262.72511.14112.21090.10790.161-0.45110.16410.0738-0.72640.65450.3628-0.18180.5407-0.0866-0.10590.2706-0.01690.67882.829943.190366.5274
40.4497-0.5701-0.19133.08811.94692.46880.04-0.02990.13180.1176-0.16590.50440.138-0.73010.12590.2149-0.1262-0.01390.41780.01210.549735.55867.580874.3977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 701
2X-RAY DIFFRACTION2B1 - 701
3X-RAY DIFFRACTION3C-1 - 701
4X-RAY DIFFRACTION4D-1 - 701

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