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- PDB-1upu: STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE, MUTANT C128V, ... -

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Basic information

Entry
Database: PDB / ID: 1upu
TitleSTRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE, MUTANT C128V, BOUND TO PRODUCT URIDINE-1-MONOPHOSPHATE (UMP)
ComponentsURACIL PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE
Function / homology
Function and homology information


uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / GTP binding
Similarity search - Function
Uracil phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / URIDINE-5'-MONOPHOSPHATE / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSchumacher, M.A. / Carter, D. / Scott, D. / Roos, D. / Ullman, B. / Brennan, R.G.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
Authors: Schumacher, M.A. / Carter, D. / Scott, D.M. / Roos, D.S. / Ullman, B. / Brennan, R.G.
History
DepositionApr 16, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_validate_close_contact / 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 / _pdbx_database_status.process_site / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: URACIL PHOSPHORIBOSYLTRANSFERASE
C: URACIL PHOSPHORIBOSYLTRANSFERASE
B: URACIL PHOSPHORIBOSYLTRANSFERASE
A: URACIL PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,84912
Polymers102,1724
Non-polymers1,6778
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16000 Å2
ΔGint-90 kcal/mol
Surface area34190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 141.770, 71.420
Angle α, β, γ (deg.)90.00, 114.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
URACIL PHOSPHORIBOSYLTRANSFERASE / UPRTASE


Mass: 25543.012 Da / Num. of mol.: 4 / Mutation: C128V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q26998, uracil phosphoribosyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STRUCTURE HAS THREE SULPHATE MOLECULES (USED IN THE CRYSTALLIZATION). ONE SULPHATE IS BOUND IN ...THE STRUCTURE HAS THREE SULPHATE MOLECULES (USED IN THE CRYSTALLIZATION). ONE SULPHATE IS BOUND IN THE ACTIVE SITE NEAR HELIX 5. THE SECOND SULPHATE ALSO BOUND NEAR THE ACTIVE SITE NEAR CIS-ARG RESIDUE (ARG112).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
210 mMdithiothreitol1drop
325-40 mg/mlprotein1drop
41.0 Mammonium phosphate1reservoir
50.1 Mcitrate1reservoir
60.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
DetectorDate: Aug 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å
Reflection
*PLUS
Num. obs: 32670 / % possible obs: 81 % / Num. measured all: 53734 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.85 Å / Mean I/σ(I) obs: 5.4

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Processing

SoftwareName: TNT / Version: 5E / Classification: refinement
RefinementResolution: 2.5→10 Å / σ(F): 1
Details: THERE IS A TETRAMER (CHAINS A, B, C, D) IN THE ASYMMETRIC UNIT. THE P21 SPACE GROUP CAN BE TRANSFORMED INTO C2221. WITH TWO IN THE ASU. THE STRUCTURE WAS SOLVED AS P21 FOR TECHNICAL REASONS.
RfactorNum. reflection% reflection
Rwork0.148 --
obs-32670 81 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 104 400 7656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.559
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg1.99

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