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- PDB-9haq: Crystal structure of methionine gamma-lyase from Brevibacterium s... -

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Basic information

Entry
Database: PDB / ID: 9haq
TitleCrystal structure of methionine gamma-lyase from Brevibacterium sandarakinum in complex with PLP and norleucine at pH 8.5
Components(Cystathionine gamma- ...) x 2
KeywordsLYASE / Complex / inhibitor / methionine / PLP
Function / homology
Function and homology information


homocysteine desulfhydrase / methionine gamma-lyase / cystathionine gamma-lyase activity / L-cysteine biosynthetic process via L-cystathionine / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
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 / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID / L-methionine gamma-lyase
Similarity search - Component
Biological speciesBrevibacterium sandarakinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.693 Å
AuthorsKopecny, D. / Ferchaud, N. / Briozzo, P.
Funding support Czech Republic, France, 4items
OrganizationGrant numberCountry
Other governmentFR 49271QH PHC BARRANDE
Ministry of Education, Youth and Sports of the Czech RepublicMOBILITY 8J23FR011 Czech Republic
Other privateIMEBATRACA
Agence Nationale de la Recherche (ANR)France 2023 ANR-11-IDEX-0003, Jean d'Alembert fellowship at Paris-Saclay France
CitationJournal: To Be Published
Title: Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention
Authors: Ferchaud, N. / Boyer, A. / Odegard, B. / Hentati, S. / Simonson, T. / Machover, D. / Kopecny, D. / Briozzo, P.
History
DepositionNov 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
G: Cystathionine gamma-synthase
H: Cystathionine gamma-synthase
I: Cystathionine gamma-synthase
J: Cystathionine gamma-synthase
K: Cystathionine gamma-synthase
L: Cystathionine gamma-synthase
M: Cystathionine gamma-synthase
N: Cystathionine gamma-synthase
O: Cystathionine gamma-synthase
P: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)693,35335
Polymers688,50816
Non-polymers4,84519
Water1,74797
1
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,1609
Polymers172,2984
Non-polymers8625
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19660 Å2
ΔGint-144 kcal/mol
Surface area44950 Å2
MethodPISA
2
E: Cystathionine gamma-synthase
F: Cystathionine gamma-synthase
G: Cystathionine gamma-synthase
H: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3949
Polymers172,0704
Non-polymers1,3245
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19510 Å2
ΔGint-145 kcal/mol
Surface area44100 Å2
MethodPISA
3
I: Cystathionine gamma-synthase
J: Cystathionine gamma-synthase
K: Cystathionine gamma-synthase
L: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,2608
Polymers172,2984
Non-polymers9624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19450 Å2
ΔGint-139 kcal/mol
Surface area43900 Å2
MethodPISA
4
M: Cystathionine gamma-synthase
N: Cystathionine gamma-synthase
O: Cystathionine gamma-synthase
P: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,5389
Polymers171,8424
Non-polymers1,6965
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19600 Å2
ΔGint-150 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.832, 151.945, 316.557
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Cystathionine gamma- ... , 2 types, 16 molecules ABDFHIJLPCEGKMNO

#1: Protein
Cystathionine gamma-synthase / Methionine gamma-lyase (MGL)


Mass: 43131.578 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium sandarakinum (bacteria) / Gene: SAMN04489751_4033 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H1YBL2
#2: Protein
Cystathionine gamma-synthase / Methionine gamma-lyase (MGL)


Mass: 42903.461 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium sandarakinum (bacteria) / Gene: SAMN04489751_4033 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H1YBL2

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Non-polymers , 5 types, 116 molecules

#3: Chemical
ChemComp-NLE / NORLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PY6 / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID / VITAMIN B6 COMPLEXED WITH 2-AMINO-HEXANOIC ACID


Mass: 362.315 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H23N2O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate, 0.1 M Tris-HCl pH 8.5, 28% PEG4000, 5 mM Norleucine, 1 mM PLP, cryoprotection: 10% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 10, 2021
Details: a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.693→109.612 Å / Num. obs: 120231 / % possible obs: 95.9 % / Redundancy: 13.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.225 / Rsym value: 0.216 / Net I/σ(I): 10.9
Reflection shellResolution: 2.693→2.93 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.962 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6012 / CC1/2: 0.52 / Rsym value: 1.876 / % possible all: 72.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDS20210323data reduction
Aimless0.7.7data scaling
PHASERphasing
autoPROC1.0.5data processing
Coot0.9.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.693→136.98 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 6037 -RANDOM
Rwork0.2581 ---
obs0.2591 120232 79 %-
Displacement parametersBiso mean: 90.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.9012 Å20 Å20 Å2
2---1.0532 Å20 Å2
3---0.152 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.693→136.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44724 0 441 97 45262
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00890709HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.92164190HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d26899SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes15251HARMONIC5
X-RAY DIFFRACTIONt_it90709HARMONIC10
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion6195SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact72725SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion15.41
LS refinement shellResolution: 2.693→2.84 Å
RfactorNum. reflection% reflection
Rfree0.3914 121 -
Rwork0.3346 --
obs--10.73 %
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)
11.822-0.96560.22043.90251.48524.7085-0.11840.096-1.41320.0960.27520.3757-1.41320.3757-0.15690.418-0.1838-0.0386-0.3037-0.0595-0.255726.031519.5699172.033
21.75870.413-0.48131.9563-0.38391.61610.05130.1477-0.360.14770.04460.0006-0.360.0006-0.0959-0.0221-0.0131-0.0425-0.0292-0.01690.16457.486726.506585.9697
30.5194-0.3683-0.11442.76830.40843.34390.3551-1.2971-1.5319-1.2971-0.3347-0.6968-1.5319-0.6968-0.02041.06180.25240.0621-0.52690.0661-0.503719.362618.9813136.214
42.17250.40550.07511.8301-0.14421.0783-0.1012-0.06410.1407-0.06410.1105-0.17420.1407-0.1742-0.0093-0.05-0.0271-0.01910.0450.00930.04-2.4918-4.589982.889
51.37840.3215-0.52684.33670.59474.70160.223-1.18960.0463-1.1896-0.10890.40450.04630.4045-0.11420.21510.1049-0.0492-0.2291-0.0549-0.202626.0092-13.0555135.548
62.59740.33820.06331.7032-0.25480.8456-0.1423-0.2130.3496-0.2130.03270.27360.34960.27360.1096-0.05690.04350.1461-0.0189-0.00820.293632.1023-15.237578.48
72.17360.2219-0.60191.5123-0.0380.9608-0.1257-0.0563-0.1948-0.05630.04730.4244-0.19480.42440.0784-0.1312-0.0528-0.00720.09540.04480.125141.810115.946983.0128
81.7077-0.46070.71122.7367-1.08332.1988-0.23980.8619-1.30720.86190.2206-0.418-1.3072-0.4180.01910.47170.10570.0675-0.2188-0.0306-0.199978.412221.1103115.596
91.2996-0.2578-0.2072.2061-1.27592.75960.0597-0.14370.0116-0.14370.3013-0.29660.0116-0.2966-0.361-0.210.0086-0.04240.11930.05580.126772.668-9.3195104.208
101.6562-0.08220.50682.7236-0.77183.83720.10240.74170.15710.74170.2868-0.21720.1571-0.2172-0.3892-0.090.02570.0305-0.01440.14410.001482.0762-23.2517136.586
110.3546-0.40281.02461.5805-0.32722.1817-0.25461.209-1.10311.2090.14490.1521-1.10310.15210.10970.84590.06860.0187-0.1318-0.0916-0.413586.98637.0017147.76
122.93420.2804-0.43082.0022-0.04560.8464-0.10480.026-0.13390.0260.19990.2532-0.13390.2532-0.0951-0.0096-0.0638-0.1218-0.0130.14180.026895.639126.068940.7489
132.18090.7233-0.05261.8268-0.54421.3314-0.2189-0.2640.2956-0.2640.19220.36150.29560.36150.02680.11260.02230.05420.0576-0.0436-0.0052103.642-5.536240.7945
143.36230.21490.04681.58030.44322.0503-0.0549-0.27560.9349-0.27560.1153-0.21170.9349-0.2117-0.06040.2057-0.20420.0285-0.0861-0.0177-0.091368.3461-14.353844.1354
152.06380.2197-1.14931.4595-0.18630.6875-0.11370.0099-0.09830.00990.3259-0.5671-0.0983-0.5671-0.2121-0.0321-0.1268-0.16330.05550.23240.207760.89317.449143.148
161.3216-0.92230.32693.05910.44762.639-0.10860.47050.23720.47050.17660.54360.23720.5436-0.0680.1828-0.0186-0.06710.06750.05990.022133.3599-12.4092171.093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|* }
2X-RAY DIFFRACTION2{ A|* }
3X-RAY DIFFRACTION3{ O|* }
4X-RAY DIFFRACTION4{ B|* }
5X-RAY DIFFRACTION5{ P|* }
6X-RAY DIFFRACTION6{ C|* }
7X-RAY DIFFRACTION7{ D|* }
8X-RAY DIFFRACTION8{ E|* }
9X-RAY DIFFRACTION9{ F|* }
10X-RAY DIFFRACTION10{ G|* }
11X-RAY DIFFRACTION11{ H|* }
12X-RAY DIFFRACTION12{ I|* }
13X-RAY DIFFRACTION13{ J|* }
14X-RAY DIFFRACTION14{ K|* }
15X-RAY DIFFRACTION15{ L|* }
16X-RAY DIFFRACTION16{ M|* }

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