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- PDB-9hp0: Variant R451K of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hp0
TitleVariant R451K of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Uridine 5'-monophosphate synthase Pyrimidine metabolism Homo sapiens
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKirck, L.L. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Variant R451K of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP
Authors: Kirck, L.L. / Tittmann, K.
History
DepositionDec 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0004
Polymers56,3512
Non-polymers6482
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-33 kcal/mol
Surface area19000 Å2
Unit cell
Length a, b, c (Å)70.140, 61.830, 71.390
Angle α, β, γ (deg.)90.00, 115.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase


Mass: 28175.668 Da / Num. of mol.: 2 / Mutation: R451K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 7.0, 1.7 - 1.9 M Ammonium sulfate, 10 mM Glutathion pH 8.0, 5% (w/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Nov 30, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.44→35.54 Å / Num. obs: 99073 / % possible obs: 98.91 % / Redundancy: 7 % / CC1/2: 0.999 / Rrim(I) all: 0.04425 / Net I/σ(I): 19.67
Reflection shellResolution: 1.44→1.491 Å / Num. unique obs: 9908 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→35.54 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 4948 5 %
Rwork0.1699 --
obs0.1709 98993 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 42 301 4172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174082
X-RAY DIFFRACTIONf_angle_d1.6465536
X-RAY DIFFRACTIONf_dihedral_angle_d15.1341548
X-RAY DIFFRACTIONf_chiral_restr0.193638
X-RAY DIFFRACTIONf_plane_restr0.015699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.35231640.33923116X-RAY DIFFRACTION99
1.46-1.470.33791620.31433096X-RAY DIFFRACTION99
1.47-1.490.29941670.30273176X-RAY DIFFRACTION99
1.49-1.510.2961630.27353090X-RAY DIFFRACTION99
1.51-1.530.25821640.26313128X-RAY DIFFRACTION99
1.53-1.550.29941640.24223131X-RAY DIFFRACTION99
1.55-1.570.24791630.23653088X-RAY DIFFRACTION99
1.57-1.60.25481660.21613144X-RAY DIFFRACTION99
1.6-1.620.21281640.20743111X-RAY DIFFRACTION99
1.62-1.650.24681630.20163095X-RAY DIFFRACTION99
1.65-1.680.25041640.20363119X-RAY DIFFRACTION99
1.68-1.710.24281650.20653132X-RAY DIFFRACTION99
1.71-1.740.26151640.19893102X-RAY DIFFRACTION99
1.74-1.780.22321650.19383136X-RAY DIFFRACTION99
1.78-1.810.21821650.18163122X-RAY DIFFRACTION99
1.81-1.860.22471620.17143090X-RAY DIFFRACTION99
1.86-1.90.18541640.16713119X-RAY DIFFRACTION99
1.9-1.950.18781650.15473117X-RAY DIFFRACTION98
1.95-2.010.1811610.16413094X-RAY DIFFRACTION98
2.01-2.080.19581670.17293172X-RAY DIFFRACTION99
2.08-2.150.18721640.16233114X-RAY DIFFRACTION99
2.15-2.240.18651660.15793162X-RAY DIFFRACTION99
2.24-2.340.18421660.15983148X-RAY DIFFRACTION99
2.34-2.460.17861650.15963148X-RAY DIFFRACTION99
2.46-2.620.18841650.16593125X-RAY DIFFRACTION99
2.62-2.820.18371670.17733176X-RAY DIFFRACTION99
2.82-3.10.19491670.18093172X-RAY DIFFRACTION99
3.1-3.550.181670.16273166X-RAY DIFFRACTION99
3.55-4.470.15541690.14143212X-RAY DIFFRACTION99
4.47-35.540.19371700.16633244X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -21.1821 Å / Origin y: 0.3439 Å / Origin z: 22.3332 Å
111213212223313233
T0.2484 Å20.0032 Å2-0.0057 Å2-0.1494 Å20.0084 Å2--0.2376 Å2
L1.6385 °20.194 °2-0.6079 °2-1.5132 °20.1243 °2--0.7038 °2
S0.0776 Å °0.0605 Å °-0.1112 Å °-0.2469 Å °-0.0405 Å °0.1361 Å °-0.133 Å °-0.0289 Å °-0.0334 Å °
Refinement TLS groupSelection details: all

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