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- PDB-9hol: Variant H283A of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hol
TitleVariant H283A of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP at 1.2 Angstrom resolution
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
PROLINE / URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKirck, L.L. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Variant H283A of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP at 1.2 Angstrom resolution
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

Downloads & links

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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)57,0375
Polymers56,2732
Non-polymers7633
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-34 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.340, 61.590, 71.060
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28136.613 Da / Num. of mol.: 2 / Mutation: H283A
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: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 50.51 %
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: Aug 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.2→32.85 Å / Num. obs: 169981 / % possible obs: 98.69 % / Redundancy: 6.9 % / CC1/2: 1 / Rrim(I) all: 0.04879 / Net I/σ(I): 19.16
Reflection shellResolution: 1.2→1.243 Å / Num. unique obs: 16891 / CC1/2: 0.677

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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: 1.2→32.85 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1488 8489 5 %
Rwork0.1363 --
obs0.1369 169765 98.68 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3935 0 29 549 4513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014356
X-RAY DIFFRACTIONf_angle_d1.2435931
X-RAY DIFFRACTIONf_dihedral_angle_d15.521666
X-RAY DIFFRACTIONf_chiral_restr0.091672
X-RAY DIFFRACTIONf_plane_restr0.01776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.33522830.33985360X-RAY DIFFRACTION98
1.21-1.230.30442790.30965309X-RAY DIFFRACTION98
1.23-1.240.2772830.29995361X-RAY DIFFRACTION99
1.24-1.260.26192810.27075339X-RAY DIFFRACTION98
1.26-1.280.24232800.25975344X-RAY DIFFRACTION98
1.28-1.290.24672820.23215343X-RAY DIFFRACTION98
1.29-1.310.25512810.24015358X-RAY DIFFRACTION98
1.31-1.330.19972790.20325305X-RAY DIFFRACTION98
1.33-1.350.19222790.19065299X-RAY DIFFRACTION98
1.35-1.370.17822850.18885404X-RAY DIFFRACTION99
1.37-1.40.1772790.17245293X-RAY DIFFRACTION98
1.4-1.420.17762830.16875381X-RAY DIFFRACTION99
1.42-1.450.16492810.16225340X-RAY DIFFRACTION99
1.45-1.480.17972820.14655373X-RAY DIFFRACTION99
1.48-1.510.1442820.14165372X-RAY DIFFRACTION99
1.51-1.550.11942860.12365430X-RAY DIFFRACTION99
1.55-1.590.12232820.11565354X-RAY DIFFRACTION99
1.59-1.630.13092830.10575372X-RAY DIFFRACTION99
1.63-1.680.1062810.10415330X-RAY DIFFRACTION98
1.68-1.730.11372820.10175359X-RAY DIFFRACTION99
1.73-1.790.11432840.10615393X-RAY DIFFRACTION99
1.79-1.860.11522860.10615439X-RAY DIFFRACTION99
1.86-1.950.11952830.11865372X-RAY DIFFRACTION99
1.95-2.050.12132850.11225418X-RAY DIFFRACTION99
2.05-2.180.13022820.11175352X-RAY DIFFRACTION99
2.18-2.350.11942850.12235402X-RAY DIFFRACTION98
2.35-2.580.13772850.11845410X-RAY DIFFRACTION99
2.58-2.960.15752850.13525423X-RAY DIFFRACTION99
2.96-3.730.15622880.13465493X-RAY DIFFRACTION100
3.73-32.850.15472930.13665548X-RAY DIFFRACTION99

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