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- PDB-4l61: Crystal structure of the Candida albicans Methionine Synthase in ... -

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Basic information

Entry
Database: PDB / ID: 4l61
TitleCrystal structure of the Candida albicans Methionine Synthase in complex with 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 / symbiont-mediated perturbation of host immune response / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / adenine biosynthetic process / hyphal cell wall / 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 / symbiont-mediated perturbation of host immune response / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / adenine biosynthetic process / hyphal cell wall / 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
METHIONINE / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 11, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,4043
Polymers88,1891
Non-polymers2152
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.490, 97.216, 97.862
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-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
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, 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: 2.1→49 Å / Num. all: 42003 / Num. obs: 42001 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.7
Reflection shellResolution: 2.13→2.17 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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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: 2.13→48.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.023 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 2117 5 %RANDOM
Rwork0.17585 ---
obs0.17867 39823 99.84 %-
all-42003 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0 Å2
2---0.9 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.13→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 10 332 6043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195858
X-RAY DIFFRACTIONr_bond_other_d0.0010.025467
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9637983
X-RAY DIFFRACTIONr_angle_other_deg0.879312555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42524.711242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76715921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3681527
X-RAY DIFFRACTIONr_chiral_restr0.1010.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021281
LS refinement shellResolution: 2.131→2.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 145 -
Rwork0.185 2885 -
obs--98.38 %
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)
11.0827-0.63630.31041.5754-0.57291.42820.09990.1630.3775-0.0684-0.1246-0.1194-0.26590.06230.02470.1432-0.0010.03850.06570.06150.144327.44914.6367-6.9989
21.2899-0.21420.07521.4883-0.11141.42770.0361-0.09630.010.08940.01690.0961-0.0269-0.0705-0.05290.0147-0.00750.00970.04250.02440.033424.1427-0.66314.3276
34.5786-0.8851-1.92420.27740.51391.27080.15320.20790.1135-0.1247-0.0503-0.0709-0.1512-0.0598-0.10290.15850.01660.01240.07940.00870.047949.7513-8.6204-22.2815
43.2206-3.8851-5.46985.76795.360310.7377-0.1384-0.143-0.08480.0683-0.09620.02860.27980.50480.23460.1080.0439-0.01220.28790.00640.06546.7002-8.6770.3471
56.3-0.5324-1.54721.9303-0.23371.34480.4138-1.1981.6830.1530.0387-0.3057-0.44110.4796-0.45250.2584-0.11930.14010.3175-0.36060.502161.94732.997-14.2235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 148
2X-RAY DIFFRACTION2A149 - 403
3X-RAY DIFFRACTION3A404 - 617
4X-RAY DIFFRACTION4A618 - 640
5X-RAY DIFFRACTION5A641 - 767

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