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- PDB-7nl1: Crystal structure of cystathionine gamma-lyase from Toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 7nl1
TitleCrystal structure of cystathionine gamma-lyase from Toxoplasma gondii
ComponentsCystathione gamma lyase, putative
KeywordsCYTOSOLIC PROTEIN / transsulfuration pathway / cysteine / hydrogen sulfide / PLP dependent
Function / homology
Function and homology information


L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cystathione gamma lyase, putative
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.331 Å
AuthorsFernandez-Rodriguez, C. / Conter, C. / Recio, I. / Astegno, A. / Martinez-Cruz, L.A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BES-2017-080435 Spain
Ministry of Economy and Competitiveness (MINECO)PID2019-109055RB-I00 Spain
CitationJournal: Protein Sci. / Year: 2023
Title: Structural basis of the inhibition of cystathionine gamma-lyase from Toxoplasma gondii by propargylglycine and cysteine.
Authors: Fernandez-Rodriguez, C. / Conter, C. / Oyenarte, I. / Favretto, F. / Quintana, I. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.A.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathione gamma lyase, putative
C: Cystathione gamma lyase, putative
D: Cystathione gamma lyase, putative
E: Cystathione gamma lyase, putative
F: Cystathione gamma lyase, putative
G: Cystathione gamma lyase, putative
H: Cystathione gamma lyase, putative
B: Cystathione gamma lyase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,82916
Polymers367,8528
Non-polymers1,9778
Water23,2751292
1
A: Cystathione gamma lyase, putative
C: Cystathione gamma lyase, putative
D: Cystathione gamma lyase, putative
B: Cystathione gamma lyase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,9158
Polymers183,9264
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25600 Å2
ΔGint-152 kcal/mol
Surface area46500 Å2
MethodPISA
2
E: Cystathione gamma lyase, putative
F: Cystathione gamma lyase, putative
G: Cystathione gamma lyase, putative
H: Cystathione gamma lyase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,9158
Polymers183,9264
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25510 Å2
ΔGint-150 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.530, 138.991, 472.997
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Cystathione gamma lyase, putative


Mass: 45981.520 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: TGME49_312930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125YN40, cystathionine gamma-lyase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 12% PEG 3350, 0.1M sodium citrate pH 4.6

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.331→48.446 Å / Num. obs: 177123 / % possible obs: 100 % / Redundancy: 19.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.036 / Rrim(I) all: 0.157 / Net I/σ(I): 19 / Num. measured all: 3461898
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.331-2.37120.41.19217872687540.8080.2721.2233.1100
6.323-48.44617.60.04716353292890.9990.0110.04947.599.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp


Resolution: 2.331→48.446 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 8762 4.95 %
Rwork0.1739 168217 -
obs0.1757 176979 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.11 Å2 / Biso mean: 51.2084 Å2 / Biso min: 26.96 Å2
Refinement stepCycle: final / Resolution: 2.331→48.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24231 0 120 1292 25643
Biso mean--43.09 58.21 -
Num. residues----3166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3311-2.35760.30232870.25915578
2.3576-2.38530.27212630.24875561
2.3853-2.41440.30652790.23955591
2.4144-2.4450.27113190.2385499
2.445-2.47710.30462930.23775617
2.4771-2.51110.26682700.22665486
2.5111-2.5470.25033120.21115604
2.547-2.5850.23832990.20235526
2.585-2.62540.25452970.20635613
2.6254-2.66840.25412810.21485525
2.6684-2.71440.23032960.20475521
2.7144-2.76380.25422990.20895660
2.7638-2.81690.26842920.20585534
2.8169-2.87440.24483010.19735544
2.8744-2.93690.26952620.20385695
2.9369-3.00520.24893030.1975485
3.0052-3.08030.23822950.19165585
3.0803-3.16360.23272650.19185662
3.1636-3.25670.23732850.18685590
3.2567-3.36180.21772950.17925603
3.3618-3.48190.193020.17145606
3.4819-3.62130.21272910.16955596
3.6213-3.7860.19422950.16225578
3.786-3.98550.18083170.15575597
3.9855-4.23510.18142770.1525682
4.2351-4.56190.17792710.13935643
4.5619-5.02050.17782640.13695704
5.0205-5.7460.17433230.15695686
5.746-7.23550.21213070.16815753
7.2355-48.4460.16433220.14975893
Refinement TLS params.Method: refined / Origin x: 12.1136 Å / Origin y: 33.8973 Å / Origin z: 57.4558 Å
111213212223313233
T0.2783 Å2-0.0536 Å20.0589 Å2-0.2942 Å2-0.0639 Å2--0.3561 Å2
L0.1049 °2-0.0057 °20.0015 °2-0.1873 °2-0.0536 °2--0.5611 °2
S-0.0499 Å °0.035 Å °-0.0118 Å °0.0105 Å °0.0122 Å °-0.0139 Å °0.0219 Å °0.0157 Å °0.0371 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA21 - 519
2X-RAY DIFFRACTION1allC19 - 519
3X-RAY DIFFRACTION1allD18 - 519
4X-RAY DIFFRACTION1allE21 - 519
5X-RAY DIFFRACTION1allF21 - 519
6X-RAY DIFFRACTION1allG21 - 519
7X-RAY DIFFRACTION1allH19 - 519
8X-RAY DIFFRACTION1allW1 - 1725
9X-RAY DIFFRACTION1allB22 - 519

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