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- PDB-9hif: Crystal Structure of Human cystathionine beta-synthase variant R336C -

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Basic information

Entry
Database: PDB / ID: 9hif
TitleCrystal Structure of Human cystathionine beta-synthase variant R336C
ComponentsCystathionine beta-synthase
KeywordsLYASE / R336C / homocysteine / synthase / trassulfuration / LIGASE
Function / homology
Function and homology information


Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / L-serine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / cysteine biosynthetic process via cystathionine / homocysteine metabolic process / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / L-serine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / cysteine biosynthetic process via cystathionine / homocysteine metabolic process / 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-cysteine catabolic process / cysteine biosynthetic process / cerebellum morphogenesis / transsulfuration / endochondral ossification / DNA protection / nitric oxide binding / cysteine biosynthetic process from serine / response to folic acid / S-adenosyl-L-methionine binding / regulation of JNK cascade / nitrite reductase (NO-forming) activity / superoxide metabolic process / blood vessel remodeling / maternal process involved in female pregnancy / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / heme binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / identical protein 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. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...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. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsConter, C. / Martinez-Cruz, L.A. / Fernandez-Rodriguez, C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-141748OB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-109055RB-I00 Spain
CitationJournal: Febs J. / Year: 2025
Title: The disease-linked R336C mutation in cystathionine beta-synthase disrupts communication with the PLP cofactor, yet maintains the enzyme's overall structural integrity.
Authors: Conter, C. / Nunez-Franco, R. / Al-Sadeq, D.W. / Fernandez-Rodriguez, C. / Goikoetxea-Usandizaga, N. / Nasrallah, G.K. / Nomikos, M. / Martinez-Chantar, M.L. / Astegno, A. / Jimenez-Oses, G. ...Authors: Conter, C. / Nunez-Franco, R. / Al-Sadeq, D.W. / Fernandez-Rodriguez, C. / Goikoetxea-Usandizaga, N. / Nasrallah, G.K. / Nomikos, M. / Martinez-Chantar, M.L. / Astegno, A. / Jimenez-Oses, G. / Martinez-Cruz, L.A.
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7304
Polymers119,4972
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-75 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.089, 139.024, 169.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 41 through 208 or resid 210 through 550 or resid 601 through 602))
d_2ens_1(chain "B" and (resid 41 through 208 or resid 210 through 550 or resid 601 through 602))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROTRPTRPAA41 - 20841 - 208
d_12LEULEUGLNGLNAA210 - 550210 - 540
d_13LLPLLPLLPLLPAA119119
d_14HEMHEMHEMHEMAC601
d_21PROPROTRPTRPBB41 - 20841 - 208
d_22LEULEUGLNGLNBB210 - 550210 - 540
d_23LLPLLPLLPLLPBB119119
d_24HEMHEMHEMHEMBD601

NCS oper: (Code: givenMatrix: (0.322685480711, 0.945866879926, 0.0347839905407), (0.945700737908, -0.323708910947, 0.0293709940801), (0.0390409382271, 0.0234176521781, -0.998963171848)Vector: 12. ...NCS oper: (Code: given
Matrix: (0.322685480711, 0.945866879926, 0.0347839905407), (0.945700737908, -0.323708910947, 0.0293709940801), (0.0390409382271, 0.0234176521781, -0.998963171848)
Vector: 12.9525843505, -14.9512554233, -78.2860797806)

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Components

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


Mass: 59748.270 Da / Num. of mol.: 2 / Mutation: R336C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli (E. coli) / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.52 % / Description: Thin needles
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 16% (wt/vol) PEG 3350 and 3% Tacsimate

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→46.7 Å / Num. obs: 16936 / % possible obs: 99.68 % / Redundancy: 10 % / CC1/2: 0.992 / CC star: 0.998 / Rpim(I) all: 0.153 / Net I/σ(I): 8.1
Reflection shellResolution: 3.65→3.78 Å / Rmerge(I) obs: 0.5358 / Mean I/σ(I) obs: 8.08 / Num. unique obs: 16936 / Rpim(I) all: 0.153 / Rrim(I) all: 0.5576 / % possible all: 99.68

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Processing

Software
NameVersionClassification
EDNA1data collection
MOLREPphasing
Coot0.9.8.93model building
PHENIX1.19.1-4122refinement
REFMAC5refinement
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.65→46.7 Å / SU ML: 0.3891 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 855 5.05 %
Rwork0.2112 16063 -
obs0.2124 16918 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.99 Å2
Refinement stepCycle: LAST / Resolution: 3.65→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7608 0 116 0 7724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957906
X-RAY DIFFRACTIONf_angle_d1.451210750
X-RAY DIFFRACTIONf_chiral_restr0.06471216
X-RAY DIFFRACTIONf_plane_restr0.01281372
X-RAY DIFFRACTIONf_dihedral_angle_d9.48041082
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.141806219354 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.880.30891310.29742615X-RAY DIFFRACTION99.1
3.88-4.180.28251360.26332652X-RAY DIFFRACTION99.86
4.18-4.60.24241460.22172648X-RAY DIFFRACTION99.96
4.6-5.260.21141460.19362661X-RAY DIFFRACTION99.89
5.26-6.630.2251580.21242688X-RAY DIFFRACTION99.96
6.63-100.21051380.16962799X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: -19.6185517284 Å / Origin y: -26.2105241598 Å / Origin z: -39.8640750622 Å
111213212223313233
T0.601902802973 Å2-0.0225351167599 Å20.0397333424512 Å2-0.509470126345 Å2-0.0236076523759 Å2--0.678075260142 Å2
L1.01290748355 °20.0773136479629 °2-0.354499252827 °2-0.333317866964 °2-0.165769710031 °2--2.30707500432 °2
S0.13101636729 Å °-0.0252139271525 Å °0.162818025256 Å °0.04795103743 Å °-0.0328706390956 Å °0.0993977639574 Å °0.00971843346935 Å °-0.0998553989738 Å °1.65537237168E-12 Å °
Refinement TLS groupSelection details: all

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