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- PDB-4l65: Crystal structure of the Candida albicans Methionine Synthase in ... -

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Basic information

Entry
Database: PDB / ID: 4l65
TitleCrystal structure of the Candida albicans Methionine Synthase in complex with 5-Methyl-Tetrahydrofolate and Methionine
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / cobalamin-independent / surface entropy reduction / fungal / Dual TIM Barrels / Methionine synthase
Function / homology
Function and homology information


L-methionine biosynthetic process from homoserine via O-acetyl-L-homoserine and cystathionine / : / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / hyphal cell wall / adenine biosynthetic process / methionine metabolic process / 'de novo' L-methionine biosynthetic process / fungal-type cell wall ...L-methionine biosynthetic process from homoserine via O-acetyl-L-homoserine and cystathionine / : / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / hyphal cell wall / adenine biosynthetic process / methionine metabolic process / 'de novo' L-methionine biosynthetic process / fungal-type cell wall / methionine biosynthetic process / cellular response to heat / methylation / cell surface / zinc ion binding / nucleus
Similarity search - Function
Cobalamin-independent methionine synthase / Cobalamin-independent methionine synthase MetE, N-terminal / Cobalamin-independent synthase, N-terminal domain / Cobalamin-independent methionine synthase MetE, C-terminal/archaeal / Cobalamin-independent synthase, Catalytic domain / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / METHIONINE / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsUbhi, D. / Robertus, J.D.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural analysis of a fungal methionine synthase with substrates and inhibitors.
Authors: Ubhi, D. / Kago, G. / Monzingo, A.F. / Robertus, J.D.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8634
Polymers88,1891
Non-polymers6743
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.926, 98.940, 100.884
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 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Cobalamin-independent methionine synthase / Methionine synthase / vitamin-B12 independent isozyme


Mass: 88188.961 Da / Num. of mol.: 1 / Mutation: K103A, K104A, E107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: BWP17 / Gene: CaO19.10083, CaO19.2551, MET6 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P82610, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM NaI, 27% (w/v) PEG 3350, 0.25 mM DTT, 0.15 mM ZnSO4, 5 mM 5-Methyl-Tetrahydrofolate-Glu3, 10 mM Methionine, 20 mM Tris-Cl pH 7.4 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2012 / Details: Asymmetric cut single crystal Si (220)
RadiationMonochromator: Asymmetric cut single crystal Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.3→49.52 Å / Num. all: 34148 / Num. obs: 34134 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11
Reflection shellResolution: 2.33→2.37 Å / Rmerge(I) obs: 0.549 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→49.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.051 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27515 1723 5.1 %RANDOM
Rwork0.20541 ---
obs0.20892 32355 99.39 %-
all-34148 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0 Å2
2---2.54 Å20 Å2
3---3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 43 137 5753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195746
X-RAY DIFFRACTIONr_bond_other_d0.0010.025166
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9637844
X-RAY DIFFRACTIONr_angle_other_deg0.866311840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41524.793242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1915831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3791525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021289
LS refinement shellResolution: 2.314→2.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 101 -
Rwork0.219 2232 -
obs--92.76 %
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)
11.3189-0.15110.31482.79430.19831.8116-0.0802-0.303-0.20781.0044-0.02830.25610.45110.05150.10850.45210.01540.13080.1050.03940.1111-7.191616.2754-12.6169
21.0951-0.19030.15064.07010.72441.9781-0.0664-0.0222-0.0030.2517-0.06620.0865-0.11540.1090.13260.0343-0.0180.00960.05180.0130.0843-4.677728.8887-25.426
34.2254-0.0109-0.70242.99550.13571.328-0.0552-0.5618-0.47380.28230.11590.26350.24940.1305-0.06070.1558-0.0034-0.03690.15040.06730.1164-33.2971-0.498-33.2632
42.43210.64940.64521.21540.05580.1927-0.0908-0.12230.0948-0.01190.10170.10040.0028-0.0635-0.01080.105-0.0372-0.03830.1196-0.00680.1858-27.19498.6999-36.0545
55.8847-1.2972-0.38774.94180.34191.117-0.163-1.5650.46851.02070.17060.55230.02590.063-0.00760.3774-0.05540.0850.6655-0.15270.3521-41.738313.1457-22.2809
66.36817.3582.49148.84271.60596.08810.3966-0.73811.02720.6888-0.57811.2326-0.5776-0.74240.18151.06630.05440.08441.35190.08990.6614-44.78370.299-13.9187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 138
2X-RAY DIFFRACTION2A139 - 403
3X-RAY DIFFRACTION3A404 - 516
4X-RAY DIFFRACTION4A517 - 655
5X-RAY DIFFRACTION5A656 - 742
6X-RAY DIFFRACTION6A743 - 767

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