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- PDB-1sd2: STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE ... -

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Basic information

Entry
Database: PDB / ID: 1sd2
TitleSTRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-METHYLTHIOTUBERCIDIN
Components5'-methylthioadenosine phosphorylase
KeywordsTRANSFERASE / METHYLTHIOADENOSINE PHOSPHORYLASE / PURINE NUCLEOSIDE PHOSPHORYLASE / PURINE SALVAGE / 5'-METHYLTHIOTUBERCIDIN / MTT / SULFATE
Function / homology
Function and homology information


Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MTH / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, J.E. / Settembre, E.C. / Cornell, K.A. / Riscoe, M.K. / Sufrin, J.R. / Ealick, S.E. / Howell, P.L.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Comparison of MTA Phosphorylase and MTA/AdoHcy Nucleosidase Explains Substrate Preferences and Identifies Regions Exploitable for Inhibitor Design.
Authors: Lee, J.E. / Settembre, E.C. / Cornell, K.A. / Riscoe, M.K. / Sufrin, J.R. / Ealick, S.E. / Howell, P.L.
History
DepositionFeb 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The I -> V conflict for residue 56 is noted in Swiss-Prot entry Q13126.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6693
Polymers31,2771
Non-polymers3922
Water2,720151
1
A: 5'-methylthioadenosine phosphorylase
hetero molecules

A: 5'-methylthioadenosine phosphorylase
hetero molecules

A: 5'-methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0089
Polymers93,8313
Non-polymers1,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9320 Å2
ΔGint-112 kcal/mol
Surface area28330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.5, 119.5, 44.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number150
Space group name H-MP321
DetailsTHE BIOLOGICAL ASSEMBLY IS A TRIMER.

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Components

#1: Protein 5'-methylthioadenosine phosphorylase / MTA phosphorylase / MTAPase


Mass: 31277.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTAP, MSAP / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MTH / 2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 5'-DEOXY-5'-(METHYLTHIO)-TUBERCIDIN


Mass: 296.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N4O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 12% (W/V) PEG 6000, 25%(V/V) ETHYLENE GLYCOL, 0.2M Tris-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2001 / Details: mirrors, monochromater
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 19929 / Num. obs: 19885 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.9
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.7 / % possible all: 75

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.207 1390 7%
Rwork0.186 --
all0.186 19929 -
obs0.186 19885 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 25 151 2198

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