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- PDB-4qqu: Crystal structure of the cobalamin-independent methionine synthas... -

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Basic information

Entry
Database: PDB / ID: 4qqu
TitleCrystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / cobalamin-independent / surface entropy reduction / fungal / dual TIM barrels / methionine synthase / closed conformation
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 / methionine synthase activity / 'de novo' L-methionine biosynthetic process ...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 / methionine synthase activity / 'de novo' L-methionine biosynthetic process / fungal-type cell wall / methionine biosynthetic process / cellular response to heat / methylation / cell surface / zinc ion binding / extracellular region / nucleus / cytosol
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
N-[4-({[(6S)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GAMMA-GLUTAMYL-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID / Chem-39S / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / PHOSPHATE ION / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsUbhi, D.K. / Robertus, J.D.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: The cobalamin-independent methionine synthase enzyme captured in a substrate-induced closed conformation.
Authors: Ubhi, D.K. / Robertus, J.D.
History
DepositionJun 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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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)89,2836
Polymers88,1891
Non-polymers1,0945
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.978, 99.102, 103.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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 (yeast) / Strain: BWP17 / Gene: CaO19.10083, CaO19.2551, MET6 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P82610, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase

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Non-polymers , 5 types, 46 molecules

#2: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-39S / N-[4-({[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-gamma-glutamyl-L-glutamic acid


Type: peptide-like, Peptide-like / Class: Unknown / Mass: 703.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37N9O12
References: N-[4-({[(6S)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GAMMA-GLUTAMYL-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM sodium iodide, 27% w/v PEG3350, 0.25 mM BME, 0.15 mM zinc sulfate, 2 mM homocysteine, 5 mM 5-methyltetrahydrofolate triglutamate, 20 mM Tris-Cl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Feb 15, 2014
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: 2.98→71.71 Å / Num. all: 16415 / Num. obs: 16414 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 5.4
Reflection shellResolution: 2.98→3.03 Å / Rmerge(I) obs: 0.601 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L5Z

4l5z


Resolution: 2.98→71.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.844 / SU B: 47.155 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 828 5.1 %RANDOM
Rwork0.17544 ---
obs0.18041 15543 99.93 %-
all-16415 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.671 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0 Å2-0 Å2
2--2.53 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.98→71.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 69 41 5998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196082
X-RAY DIFFRACTIONr_bond_other_d0.0010.025660
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9728279
X-RAY DIFFRACTIONr_angle_other_deg0.832313003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4524.624266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55115967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5941532
X-RAY DIFFRACTIONr_chiral_restr0.0790.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021354
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_it0.7621.9423064
X-RAY DIFFRACTIONr_mcbond_other0.7611.9423064
X-RAY DIFFRACTIONr_mcangle_it1.3032.913825
X-RAY DIFFRACTIONr_mcangle_other2.7594.6963821
X-RAY DIFFRACTIONr_scbond_it0.722.0173018
X-RAY DIFFRACTIONr_scbond_other1.4263.1913000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4344.7444430
X-RAY DIFFRACTIONr_long_range_B_refined4.23424.7727174
X-RAY DIFFRACTIONr_long_range_B_other4.23424.7717175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.98→3.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 64 -
Rwork0.257 1119 -
obs--99.5 %
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)
11.351-0.1491-0.22270.85140.01781.19650.1065-0.10890.1058-0.1044-0.01330.061-0.06520.0595-0.09320.1039-0.01810.0020.0316-0.03350.04087.9301-20.2463-31.196
21.0541-0.0018-0.4960.6083-0.17221.09450.0141-0.3476-0.128-0.0361-0.0851-0.0374-0.02260.40320.0710.04990.02240.00210.21810.04920.01830.2596-37.3515-21.3185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 379
2X-RAY DIFFRACTION2A380 - 767

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