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- PDB-1uou: Crystal structure of human thymidine phosphorylase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1uou
TitleCrystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor
ComponentsTHYMIDINE PHOSPHORYLASE
KeywordsTRANSFERASE / PHOSPHORYLASE / GLYCOSYLTRANSFERASE / CHEMOTAXIS / ANGIOGENESIS
Function / homology
Function and homology information


thymidine phosphorylase / regulation of gastric motility / dTMP catabolic process / pyrimidine nucleoside metabolic process / regulation of transmission of nerve impulse / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / Pyrimidine salvage / Pyrimidine catabolism ...thymidine phosphorylase / regulation of gastric motility / dTMP catabolic process / pyrimidine nucleoside metabolic process / regulation of transmission of nerve impulse / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / Pyrimidine salvage / Pyrimidine catabolism / : / regulation of myelination / growth factor activity / chemotaxis / angiogenesis / cell differentiation / protein homodimerization activity / cytosol
Similarity search - Function
Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C ...Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CMU / Thymidine phosphorylase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsNorman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / McAlister, M.S.B. / McCall, E.J. ...Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / McAlister, M.S.B. / McCall, E.J. / McMiken, H.H.J. / Paterson, D.S. / Timms, D. / Tucker, J.A. / Pauptit, R.A.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of Human Thymidine Phosphorylase in Complex with a Small Molecule Inhibitor
Authors: Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / Mcalister, M.S.B. / Mccall, E.J. / Mcmicken, H.H.J. / Paterson, D.S. / Timms, ...Authors: Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / Mcalister, M.S.B. / Mccall, E.J. / Mcmicken, H.H.J. / Paterson, D.S. / Timms, D. / Tucker, J.A. / Pauptit, R.A.
History
DepositionSep 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4382
Polymers49,1951
Non-polymers2431
Water1,35175
1
A: THYMIDINE PHOSPHORYLASE
hetero molecules

A: THYMIDINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8764
Polymers98,3912
Non-polymers4852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)69.990, 66.090, 96.870
Angle α, β, γ (deg.)90.00, 106.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

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Components

#1: Protein THYMIDINE PHOSPHORYLASE / TDRPASE / TP / PLATELET-DERIVED ENDOTHELIAL CELL GROWTH FACTOR / PD-ECGF / GLIOSTATIN


Mass: 49195.363 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-408,411-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMOAL-10T / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19971, thymidine phosphorylase
#2: Chemical ChemComp-CMU / 5-CHLORO-6-(1-(2-IMINOPYRROLIDINYL) METHYL) URACIL / 5-CHLORO-6-[(2-IMINOPYRROLIDIN-1-YL)METHYL]PYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 242.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11ClN4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPYRIMIDINE NUCLEOSIDE METABOLISM, ALSO KNOWN AS PLATELET- DERIVED ENDOTHELIAL CELL GROWTH FACTOR ...PYRIMIDINE NUCLEOSIDE METABOLISM, ALSO KNOWN AS PLATELET- DERIVED ENDOTHELIAL CELL GROWTH FACTOR (PD-ECGF), OVEREXPRESSED IN CERTAIN SOLID TUMOURS. CATALYZES THE REVERSIBLE PHOSPHOROLYSIS OF THYMIDINE. EXISTS AS A HOMODIMER.

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 6.5
Details: 8% PEG 1000(W/V), 50MM MALATE/IMIDAZOLE PH 6.5,100MM MGCL2.
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.4
250 mM1dropNaCl
38 mg/mlprotein1drop
48 %(w/v)PEG10001reservoir
550 mMmalate/imidazole1reservoirpH6.5
6100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.11→91.3 Å / Num. obs: 15827 / % possible obs: 63.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.5
Reflection shellResolution: 2.11→2.21 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 1.8 / % possible all: 11.2
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 91.3 Å / Redundancy: 2.1 % / Num. measured all: 32998 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 11.2 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRW, CHAIN B

1brw


Resolution: 2.11→91.29 Å / SU B: 9.266 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.301
Details: RESIDUES 409-410 WERE REMOVED BY PROTEOLYSIS.RESIDUES 12-32, 238-239, 407-414 AND 481-482 WERE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 855 5.4 %RANDOM
Rwork0.188 ---
obs0.192 14966 64.37 %-
Displacement parametersBiso mean: 22.984 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å21.6 Å2
2--0.6 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.11→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 16 75 3279
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 91.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.577 / Rfactor Rwork: 0.348

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