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- PDB-2nmp: Crystal structure of human Cystathionine gamma lyase -

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Basic information

Entry
Database: PDB / ID: 2nmp
TitleCrystal structure of human Cystathionine gamma lyase
ComponentsCystathionine gamma-lyase
KeywordsLYASE / amino-acid biosynthesis / pyridoxal phopshate / structural genomics / Structural Genomics Consortium / SGC
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
PYRIDOXAL-5'-PHOSPHATE / Cystathionine gamma-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKarlberg, T. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Karlberg, T. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Hogbom, M. / Johansson, I. / Kotenyova, T. / Magnusdottir, A. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / van-den-Berg, S. / Wallden, K. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S
Authors: Sun, Q. / Collins, R. / Huang, S. / Holmberg-Schiavone, L. / Anand, G.S. / Tan, C.-H. / van-den-Berg, S. / Deng, L.-W. / Moore, P.K. / Karlberg, T. / Sivaraman, J.
History
DepositionOct 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,0847
Polymers177,3434
Non-polymers7413
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19940 Å2
ΔGint-117 kcal/mol
Surface area45990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.780, 107.570, 153.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 6

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA10 - 4911 - 50
21GLNGLNBB10 - 4911 - 50
31GLNGLNCC10 - 4911 - 50
41GLNGLNDD10 - 4911 - 50
12PROPROAA64 - 39965 - 400
22PROPROBB64 - 39965 - 400
32PROPROCC64 - 39965 - 400
42PROPRODD64 - 39965 - 400

NCS ensembles :
ID
1
2

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Components

#1: Protein
Cystathionine gamma-lyase / / Gamma-cystathionase


Mass: 44335.672 Da / Num. of mol.: 4 / Fragment: residues 1-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) / References: UniProt: P32929
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% PEG3350, 200mM Ammonium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2006
Details: liquid nitrogen cooled channel-cut silicon monochromator, a cylindrical grazing incidence mirror
RadiationMonochromator: monochromator crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 54383 / Num. obs: 54383 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Rsym value: 0.225 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5730 / Rsym value: 0.517 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N8P

1n8p


Resolution: 2.6→19.93 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.89 / SU B: 21.656 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.876 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24454 2718 5 %RANDOM
Rwork0.17694 ---
all0.18035 51628 --
obs0.18035 51628 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.756 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å20 Å2
2---0.17 Å20 Å2
3---2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11846 0 45 157 12048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212158
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.641.96416502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36451524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41324.412510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.571152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7861550
X-RAY DIFFRACTIONr_chiral_restr0.1090.21884
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029095
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.25847
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.28239
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6481.57797
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.126212306
X-RAY DIFFRACTIONr_scbond_it1.87934863
X-RAY DIFFRACTIONr_scangle_it2.9774.54196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A320loose positional0.465
12B320loose positional0.365
13C320loose positional0.335
14D320loose positional0.345
21A2480loose positional0.515
22B2480loose positional0.695
23C2480loose positional0.565
24D2480loose positional0.445
11A320loose thermal1.9410
12B320loose thermal2.0710
13C320loose thermal2.5710
14D320loose thermal1.6610
21A2480loose thermal1.8110
22B2480loose thermal2.1810
23C2480loose thermal1.8410
24D2480loose thermal1.5810
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 196 -
Rwork0.223 3728 -
obs--100 %
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)
11.44360.07340.31181.39170.47851.11360.09740.0029-0.68210.16470.1185-0.37330.36730.118-0.21590.01220.0332-0.0533-0.0170.02670.1282-7.66819.995-32.705
21.12360.28950.18291.3198-0.05921.6382-0.0125-0.1858-0.07360.2593-0.0466-0.11920.0930.05860.0591-0.02850.0246-0.038-0.04290.017-0.0483-13.37330.694-14.714
32.0184-0.31760.48631.88910.24450.8971-0.0263-0.09970.17090.1362-0.0238-0.044-0.0629-0.05120.0501-0.0747-0.0178-0.007-0.0779-0.0058-0.0296-19.83352.308-23.855
40.87760.7085-0.24783.2931-0.30340.2646-0.0006-0.0442-0.06310.22360.13760.2082-0.0358-0.1535-0.137-0.09470.03230.0163-0.06910.0115-0.0827-43.94423.375-31.727
51.35820.0768-0.05181.0013-0.07211.147-0.1376-0.3398-0.0260.24080.12720.02380.05420.09790.01030.02190.07620.02840.06030.0041-0.0817-37.62514.344-13.937
63.7355-2.9317-0.72064.8887-0.32081.1393-0.0545-0.1481-0.07090.19810.0839-0.1121-0.01470.12-0.0294-0.0051-0.0267-0.0148-0.03110.0105-0.0183-33.482-11.129-23.224
72.76211.3966-1.15481.299-0.59830.4831-0.0049-0.1277-0.5857-0.0044-0.0918-0.5220.16030.28690.09670.13640.0126-0.0190.09660.0090.1373-23.5532.662-42.326
80.8873-0.05330.08781.0259-0.03310.82780.04620.1579-0.1411-0.1307-0.0449-0.09720.15880.1471-0.0013-0.01530.0320.0134-0.0081-0.0509-0.0839-33.7867.801-59.814
91.7095-0.15360.61281.1644-0.14590.940.0089-0.0055-0.0262-0.00240.01030.22490.0346-0.0437-0.0193-0.071-0.0285-0.0225-0.10010.0021-0.0769-57.12113.687-51.866
103.54741.2337-0.70511.0814-0.11220.1673-0.1620.03920.3127-0.21810.06760.0233-0.07820.02670.0944-0.05330.0174-0.0314-0.10530.0439-0.0828-28.99638.45-43.644
110.69760.3029-0.14570.5242-0.08190.798-0.00930.1670.0612-0.07380.0133-0.040.0498-0.0058-0.004-0.03180.0270.0258-0.01590.044-0.0577-19.42832.038-61.107
122.6659-1.285-0.1981.8351-0.70521.16840.04830.1706-0.043-0.1621-0.0022-0.10410.09430.0254-0.0461-0.0401-0.02570.0248-0.0648-0.0245-0.00214.46727.034-53.512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 4911 - 50
2X-RAY DIFFRACTION2AA64 - 27065 - 271
3X-RAY DIFFRACTION3AA271 - 399272 - 400
4X-RAY DIFFRACTION4BB10 - 5211 - 53
5X-RAY DIFFRACTION5BB53 - 27054 - 271
6X-RAY DIFFRACTION6BB271 - 400272 - 401
7X-RAY DIFFRACTION7CC10 - 5211 - 53
8X-RAY DIFFRACTION8CC53 - 27054 - 271
9X-RAY DIFFRACTION9CC271 - 401272 - 402
10X-RAY DIFFRACTION10DD10 - 5211 - 53
11X-RAY DIFFRACTION11DD53 - 27054 - 271
12X-RAY DIFFRACTION12DD271 - 401272 - 402

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