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- PDB-5mms: Human cystathionine beta-synthase (CBS) p.P49L delta409-551 variant -

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Basic information

Entry
Database: PDB / ID: 5mms
TitleHuman cystathionine beta-synthase (CBS) p.P49L delta409-551 variant
ComponentsCystathionine beta-synthaseCystathionine beta synthase
KeywordsLYASE / cystathionine beta-synthase / hydrogen sulfide / transsulfuration / classical homocystinuria
Function / homology
Function and homology information


Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / cystathionine beta-synthase activity / carbon monoxide binding / hydrogen sulfide biosynthetic process ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / cystathionine beta-synthase activity / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine metabolic process / cartilage development involved in endochondral bone morphogenesis / regulation of nitric oxide mediated signal transduction / L-serine catabolic process / L-cysteine catabolic process / cysteine biosynthetic process / cysteine synthase activity / cerebellum morphogenesis / L-cysteine desulfhydrase activity / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / transsulfuration / endochondral ossification / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / maternal process involved in female pregnancy / blood vessel remodeling / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme ...Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / CBS domain / CBS domain / CBS domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVicente, J.B. / Colaco, H.G. / Malagrino, F. / Santo, P.E. / Gutierres, A. / Bandeiras, T.M. / Leandro, P. / Brito, J.A. / Giuffre, A.
Funding support Portugal, Italy, 8items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/SAU-MIC/111447/2009 Portugal
Fundacao para a Ciencia e a TecnologiaSFRH/BPD/79224/2011 Portugal
Fundacao para a Ciencia e a TecnologiaPD/BD/113990/2015 Portugal
Ministero dell'Istruzione, dell'Universit? e della RicercaPNR-CNR Aging Program 2012?2014 Italy
Ministero dell'Istruzione, dell'Universit? e della RicercaPRIN 20158EB2CM_003 Italy
y Consiglio Nazionale delle Ricerche Italy
Federation of European Biochemical Societies
Fundacao para a Ciencia e a Tecnologia e Ministerio da Ciencia e do Ensino SuperioriNOVA4Health Research Unit - LISBOA-01-0145-FEDER-007344 Portugal
CitationJournal: Oxid Med Cell Longev / Year: 2017
Title: A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine beta-Synthase: Increased CO Reactivity as a Novel Molecular Mechanism of Pathogenicity?
Authors: Vicente, J.B. / Colaco, H.G. / Malagrino, F. / Santo, P.E. / Gutierres, A. / Bandeiras, T.M. / Leandro, P. / Brito, J.A. / Giuffre, A.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jan 17, 2024Group: 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 / software / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
C: Cystathionine beta-synthase
D: Cystathionine beta-synthase
E: Cystathionine beta-synthase
F: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,65521
Polymers268,4046
Non-polymers5,25115
Water3,333185
1
C: Cystathionine beta-synthase
hetero molecules

A: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1956
Polymers89,4682
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_444x-1,y-1,z-11
2
A: Cystathionine beta-synthase
hetero molecules

C: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1956
Polymers89,4682
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_666x+1,y+1,z+11
Buried area7050 Å2
ΔGint-59 kcal/mol
Surface area26040 Å2
MethodPISA
3
B: Cystathionine beta-synthase
F: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2187
Polymers89,4682
Non-polymers1,7505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-73 kcal/mol
Surface area26240 Å2
MethodPISA
4
D: Cystathionine beta-synthase
E: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2418
Polymers89,4682
Non-polymers1,7736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-85 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.174, 86.783, 97.786
Angle α, β, γ (deg.)102.67, 103.07, 111.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cystathionine beta-synthase / Cystathionine beta synthase / Beta-thionase / Serine sulfhydrase


Mass: 44734.027 Da / Num. of mol.: 6 / Mutation: P49L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.31 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 35% w/v PEG 2000 MME 0.15 M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.8→76.35 Å / Num. obs: 58862 / % possible obs: 98.5 % / Redundancy: 2.1 % / Biso Wilson estimate: 65.48 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.112 / Rrim(I) all: 0.174 / Net I/σ(I): 4.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.62 / % possible all: 95.6

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Processing

Software
NameVersionClassification
autoPROCsnapshot20151214data collection
XDSOct 15, 2015data reduction
Aimless0.5.21data scaling
PHASERphasing
PHENIXrefinement
BUSTER2.10.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBQ

1jbq


Resolution: 2.8→76.35 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.314
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2836 4.82 %RANDOM
Rwork0.182 ---
obs0.184 58857 98.5 %-
Displacement parametersBiso mean: 45.79 Å2
Baniso -1Baniso -2Baniso -3
1--2.7003 Å2-4.6611 Å20.6853 Å2
2---3.8852 Å20.217 Å2
3---6.5855 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.8→76.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15916 0 351 185 16452
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132985HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1259892HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7199SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes395HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4828HARMONIC5
X-RAY DIFFRACTIONt_it32985HARMONIC20
X-RAY DIFFRACTIONt_nbd13SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion15.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2175SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact35942SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 220 5.07 %
Rwork0.22 4116 -
all0.223 4336 -
obs--97.86 %
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)
10.6875-0.4569-0.05940.9984-0.02190.7937-0.0079-0.0014-0.10560.0180.066-0.03440.1569-0.1384-0.0582-0.0645-0.0493-0.0583-0.0016-0.1569-0.076159.0979-18.2347131.1526
20.67610.1070.16171.2929-0.01720.80750.0770.1174-0.0077-0.0802-0.0885-0.02390.01960.05950.0115-0.07710.1144-0.06140.0115-0.1461-0.097471.7573-53.256859.5956
30.40660.23210.18020.8354-0.25351.5999-0.0054-0.02910.07220.00170.02360.0162-0.189-0.1612-0.0182-0.09770.0837-0.0555-0.0342-0.1883-0.011731.5191-38.679155.9548
40.7463-0.0067-0.18760.44970.08330.9561-0.050.05030.014-0.0222-0.01160.0599-0.013-0.0770.0616-0.01440.0427-0.1143-0.0676-0.0916-0.032362.0472-7.38781.0267
50.7209-0.2321-0.04541.22050.50111.04640.0263-0.06150.01810.03510.0782-0.1437-0.03150.1902-0.1046-0.1326-0.0185-0.08820.0513-0.1423-0.079486.9104-3.0827102.0035
61.22880.0550.09110.86520.28470.87620.0119-0.1166-0.06470.1453-0.01830.0168-0.0066-0.03910.0064-0.01070.0782-0.0815-0.0503-0.1059-0.115466.208-49.341191.6672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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