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- PDB-5eig: Engineered human cystathionine gamma lyase (E59T, E339V) to deple... -

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Basic information

Entry
Database: PDB / ID: 5eig
TitleEngineered human cystathionine gamma lyase (E59T, E339V) to deplet cysteine
Components(Cystathionine gamma-lyase) x 2
KeywordsLYASE / Cyst(e)inase
Function / homology
Function and homology information


protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / homocysteine desulfhydrase / homocysteine desulfhydrase activity / Cysteine formation from homocysteine / Degradation of cysteine and homocysteine / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) ...protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / homocysteine desulfhydrase / homocysteine desulfhydrase activity / Cysteine formation from homocysteine / Degradation of cysteine and homocysteine / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / hydrogen sulfide biosynthetic process / L-cysteine desulfhydrase activity / cysteine biosynthetic process / cysteine metabolic process / transsulfuration / negative regulation of apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to leukemia inhibitory factor / lipid metabolic process / pyridoxal phosphate binding / positive regulation of canonical NF-kappaB signal transduction / protein homotetramerization / calmodulin binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / 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 ...Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / 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
CYSTEINE / Cystathionine gamma-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsYan, W. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Texas at Austin Welch FoundationF-1778 United States
CitationJournal: To Be Published
Title: Systemic Depletion of Serum L-Cyst(e)ine with an Engineered Human Enzyme Mediates Potent Induction of ROS and Cancer Ablation
Authors: Cramer, S. / Saha, A. / Tadi, S. / Tiziani, S. / Yan, W. / Triplett, K. / Lamb, C. / Alters, S. / Johnson, D. / Zhang, Y. / DiGiovanni, J. / Georgiou, G. / Stone, E.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: 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-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
G: Cystathionine gamma-lyase
H: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,40716
Polymers358,5638
Non-polymers8448
Water11,998666
1
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6918
Polymers179,2814
Non-polymers4094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-171 kcal/mol
Surface area45100 Å2
MethodPISA
2
E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
G: Cystathionine gamma-lyase
H: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7168
Polymers179,2814
Non-polymers4344
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18930 Å2
ΔGint-153 kcal/mol
Surface area44710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.377, 163.455, 181.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Cystathionine gamma-lyase / Cysteine-protein sulfhydrase / Gamma-cystathionase


Mass: 44850.156 Da / Num. of mol.: 6 / Mutation: E59T, E339V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Production host: Escherichia coli (E. coli) / References: UniProt: P32929, cystathionine gamma-lyase
#2: Protein Cystathionine gamma-lyase / Cysteine-protein sulfhydrase / Gamma-cystathionase


Mass: 44731.020 Da / Num. of mol.: 2 / Mutation: E59T, E339V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Production host: Escherichia coli (E. coli) / References: UniProt: P32929, cystathionine gamma-lyase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES pH6.5 50-100mM Sodium Citratre 25%-30% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97733 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2013
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97733 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 92940 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rsym value: 0.14 / Net I/σ(I): 10.385
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.182 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.7→40 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 4636 5.02 %
Rwork0.1905 --
obs0.1925 92338 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24038 0 46 666 24750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424616
X-RAY DIFFRACTIONf_angle_d0.87433416
X-RAY DIFFRACTIONf_dihedral_angle_d13.2818907
X-RAY DIFFRACTIONf_chiral_restr0.0363817
X-RAY DIFFRACTIONf_plane_restr0.0054259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6977-2.72830.29371440.24942729X-RAY DIFFRACTION93
2.7283-2.76040.28311550.2482920X-RAY DIFFRACTION100
2.7604-2.79410.30931450.24582933X-RAY DIFFRACTION100
2.7941-2.82950.26841750.24672865X-RAY DIFFRACTION100
2.8295-2.86670.29071530.23152903X-RAY DIFFRACTION100
2.8667-2.90590.26641690.22972934X-RAY DIFFRACTION100
2.9059-2.94750.26291560.22132886X-RAY DIFFRACTION100
2.9475-2.99140.25621610.21952924X-RAY DIFFRACTION99
2.9914-3.03820.25371680.21642878X-RAY DIFFRACTION100
3.0382-3.0880.26081620.21352938X-RAY DIFFRACTION100
3.088-3.14120.27011530.20792922X-RAY DIFFRACTION100
3.1412-3.19830.24661420.21362915X-RAY DIFFRACTION100
3.1983-3.25980.26521670.21572921X-RAY DIFFRACTION99
3.2598-3.32640.25771530.21392918X-RAY DIFFRACTION99
3.3264-3.39870.24521710.21062894X-RAY DIFFRACTION99
3.3987-3.47770.26011520.20722899X-RAY DIFFRACTION99
3.4777-3.56470.29871290.19512978X-RAY DIFFRACTION99
3.5647-3.6610.23441370.19292913X-RAY DIFFRACTION99
3.661-3.76870.22741410.18372962X-RAY DIFFRACTION99
3.7687-3.89030.2191600.17312913X-RAY DIFFRACTION99
3.8903-4.02930.22491390.17032946X-RAY DIFFRACTION99
4.0293-4.19050.19161470.16252942X-RAY DIFFRACTION99
4.1905-4.38110.17061690.15872902X-RAY DIFFRACTION99
4.3811-4.6120.20281610.15192920X-RAY DIFFRACTION99
4.612-4.90070.19551400.16042951X-RAY DIFFRACTION98
4.9007-5.27860.19461630.15972921X-RAY DIFFRACTION98
5.2786-5.80910.22861610.17322949X-RAY DIFFRACTION99
5.8091-6.64790.22021610.19382965X-RAY DIFFRACTION98
6.6479-8.36890.19571440.16682977X-RAY DIFFRACTION98
8.3689-49.11680.20471580.17823084X-RAY DIFFRACTION96

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