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- PDB-9qm6: Crystal structure of highly stable methionine gamma-lyase from Th... -

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Basic information

Entry
Database: PDB / ID: 9qm6
TitleCrystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine
ComponentsL-methionine gamma-lyase
KeywordsLYASE / Enzyme / methionine gamma-lyase / complex / PLP / inhibitor
Function / homology
Function and homology information


homocysteine desulfhydrase activity / homocysteine desulfhydrase / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
L-methionine gamma-lyase / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
NORLEUCINE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesThermobrachium celere (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.607 Å
AuthorsKopecny, D. / Ferchaud, N. / Briozzo, P.
Funding support Czech Republic, France, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic8J23FR011 Czech Republic
Agence Nationale de la Recherche (ANR)the Jean d'Alembert fellowship as part of France 2030 program ANR-11-IDEX-0003 France
Other privateIMEBATRACA
Other governmentFR 49271QH PHC BARRANDE
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: The methioninase from the alkalithermophile Thermobrachium celere possesses suitable properties for treatment of cancer.
Authors: Ferchaud, N. / Kopecny, D. / Perina, M. / Boyer, A. / Hentati, S. / Pontoizeau, C. / Desterke, C. / Krystof, V. / Machover, D. / Briozzo, P.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
C: L-methionine gamma-lyase
D: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,3449
Polymers183,7574
Non-polymers5875
Water1267
1
A: L-methionine gamma-lyase
D: L-methionine gamma-lyase
hetero molecules

A: L-methionine gamma-lyase
D: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,40610
Polymers183,7574
Non-polymers6496
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area22100 Å2
ΔGint-114 kcal/mol
Surface area47640 Å2
MethodPISA
2
B: L-methionine gamma-lyase
C: L-methionine gamma-lyase
hetero molecules

B: L-methionine gamma-lyase
C: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,2828
Polymers183,7574
Non-polymers5254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area21670 Å2
ΔGint-129 kcal/mol
Surface area47890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.426, 86.426, 862.41
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
L-methionine gamma-lyase


Mass: 45939.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Methionine gamma-lyase (MGL) / Source: (gene. exp.) Thermobrachium celere (bacteria) / Gene: TCEL_00634 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R7RTI8, methionine gamma-lyase
#2: Chemical
ChemComp-NLE / NORLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Well solution: 26% PEG 400 and 0.1M MgCl2 in 1M MES pH 6.5 Cryoprotection: 30% PEG 400 Protein: 13.5 mg/ml in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM PLP with 5 mM norleucin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2022 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: Channel cut cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.61→143.74 Å / Num. obs: 39975 / % possible obs: 94.7 % / Redundancy: 37.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.038 / Rrim(I) all: 0.235 / Net I/σ(I): 14.8
Reflection shellResolution: 2.61→2.9 Å / Redundancy: 36.4 % / Rmerge(I) obs: 2.982 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1999 / CC1/2: 0.623 / Rpim(I) all: 0.496 / Rrim(I) all: 3.023 / % possible all: 74.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
Coot0.9.8model building
PHASER2.7phasing
XDSJune 30, 2023data reduction
STARANISO2.4.9data scaling
Aimless0.7.15data scaling
autoPROC1.0.5data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.607→37.84 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.445
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 1998 -RANDOM
Rwork0.2498 ---
obs0.2507 39943 65.7 %-
Displacement parametersBiso mean: 84.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.4075 Å20 Å20 Å2
2---1.4075 Å20 Å2
3---2.815 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.607→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12263 0 100 9 12372
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00724976HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.945227HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7499SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4001HARMONIC5
X-RAY DIFFRACTIONt_it24976HARMONIC10
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion1696SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact20223SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion15.46
LS refinement shellResolution: 2.61→2.8 Å
RfactorNum. reflection% reflection
Rfree0.4476 40 -
Rwork0.3801 --
obs0.3835 799 7.14 %
Refinement TLS params.

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)
11.57450.03690.1991.7886-0.44413.3152-0.1992-0.53150.0874-0.53150.02450.41490.08740.41490.1746-0.0093-0.18960.1376-0.0847-0.1042-0.0748-14.230937.10455.613
21.4735-0.2790.23161.87650.0322.76160.13120.16-0.56520.16-0.17680.1539-0.56520.15390.04560.2248-0.13240.0861-0.3295-0.1027-0.0206-35.080621.082313.4036
31.77090.0231-0.19981.84250.1882.16870.15710.34630.38770.3463-0.1690.17910.38770.17910.01190.2283-0.0766-0.0938-0.28240.0348-0.07146.113259.287519.4702
42.04140.08870.00361.5599-0.0932.4506-0.1799-0.60570.5457-0.60570.0732-0.73540.5457-0.73540.10670.0054-0.425-0.05310.0446-0.0654-0.0394-45.7416.991956.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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