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- PDB-5tt2: Inactive conformation of engineered human cystathionine gamma lya... -

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Basic information

Entry
Database: PDB / ID: 5tt2
TitleInactive conformation of engineered human cystathionine gamma lyase (E59N, R119L, E339V) to depleting methionine
ComponentsCystathionine gamma-lyase
KeywordsLYASE / engineered protein / methioninase / inactive form
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 / cysteine biosynthetic process / cysteine metabolic process / L-cysteine desulfhydrase activity / transsulfuration / negative regulation of apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to leukemia inhibitory factor / lipid metabolic process / pyridoxal phosphate binding / protein homotetramerization / positive regulation of canonical NF-kappaB signal transduction / 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
Cystathionine gamma-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.949 Å
AuthorsYan, W. / Zhang, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA154754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104896 United States
Welch FoundationF-1778 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structural Snapshots of an Engineered Cystathionine-gamma-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site.
Authors: Yan, W. / Stone, E. / Zhang, Y.J.
History
DepositionOct 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6046
Polymers93,2202
Non-polymers3844
Water0
1
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules

C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,20912
Polymers186,4404
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area10830 Å2
ΔGint-224 kcal/mol
Surface area49980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.224, 120.224, 125.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 46610.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P32929, cystathionine gamma-lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: SO4

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES pH6.5 20% PEG3350 200mM Na/K tartrate 200mM lithium sulfate
PH range: 6.0-7.0 / Temp details: cold room

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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: Jul 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.949→50 Å / Num. obs: 19542 / % possible obs: 97.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.949→49.429 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2542 995 5.09 %
Rwork0.2 --
obs0.2028 19542 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.949→49.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 0 0 5344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035456
X-RAY DIFFRACTIONf_angle_d0.7037404
X-RAY DIFFRACTIONf_dihedral_angle_d14.6091962
X-RAY DIFFRACTIONf_chiral_restr0.028854
X-RAY DIFFRACTIONf_plane_restr0.005934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9493-3.10480.381340.30672600X-RAY DIFFRACTION98
3.1048-3.29930.33121580.25572595X-RAY DIFFRACTION98
3.2993-3.55390.29531570.22892600X-RAY DIFFRACTION98
3.5539-3.91140.27371500.1892618X-RAY DIFFRACTION98
3.9114-4.47710.18991490.16562641X-RAY DIFFRACTION98
4.4771-5.63940.19111290.1642685X-RAY DIFFRACTION98
5.6394-49.43580.2441180.1952808X-RAY DIFFRACTION96
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)
11.3228-0.03760.35381.09110.65621.4089-0.07450.01780.42310.1356-0.0197-0.2266-0.31660.11280.05840.441-0.0873-0.10090.26950.06670.53178.6532-31.184912.7994
21.6581-0.14370.10480.76690.16461.5631-0.07040.0020.36850.1096-0.0159-0.2109-0.2497-0.05320.07450.3588-0.006-0.08090.18620.01550.384-2.4978-33.725516.2953
31.60410.52440.28552.32790.79192.44410.0541-0.55820.02520.3364-0.1888-0.0821-0.2244-0.08750.09310.47570.0339-0.11880.4048-0.06480.3887-7.6756-35.541635.6196
41.81130.08050.42811.4610.04041.58670.0533-0.0006-0.14280.0206-0.02280.170.1011-0.3564-0.00790.2546-0.01680.03640.3831-0.030.3695-30.055-62.272914.0809
50.8889-0.30190.14841.6279-0.34441.36260.0252-0.1073-0.0281-0.0035-0.01810.0932-0.0376-0.29250.02190.22420.01160.01240.3136-0.03260.3095-25.1272-51.961310.5501
62.5540.13040.90281.4064-0.09512.7888-0.00020.35940.0558-0.1854-0.1521-0.2584-0.0087-0.08340.05860.29570.08520.02050.3509-0.09950.2846-22.2089-47.3536-8.7877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 29:248 )C29 - 248
2X-RAY DIFFRACTION2( CHAIN C AND RESID 249:331 )C249 - 331
3X-RAY DIFFRACTION3( CHAIN C AND RESID 332:418 )C332 - 418
4X-RAY DIFFRACTION4( CHAIN D AND RESID 29:248 )D29 - 248
5X-RAY DIFFRACTION5( CHAIN D AND RESID 249:331 )D249 - 331
6X-RAY DIFFRACTION6( CHAIN D AND RESID 332:418 )D332 - 418

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