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- PDB-9hvv: Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in ... -

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Basic information

Entry
Database: PDB / ID: 9hvv
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with 6-Methyl 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 / cytosol / cytoplasm
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 / 6-methyluridine 5'-(dihydrogen phosphate) / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsKirck, L.L. / Rindfleisch, S. / Schmidt, T. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with 6-Methyl UMP
Authors: Kirck, L.L. / Rindfleisch, S. / Schmidt, T. / Tittmann, K.
History
DepositionJan 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8685
Polymers28,2041
Non-polymers6654
Water5,513306
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,73610
Polymers56,4072
Non-polymers1,3298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4120 Å2
ΔGint-44 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.375, 116.687, 62.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-758-

HOH

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Components

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


Mass: 28203.680 Da / Num. of mol.: 1
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-U6M / 6-methyluridine 5'-(dihydrogen phosphate)


Mass: 338.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/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: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.12→42.53 Å / Num. obs: 104066 / % possible obs: 97.02 % / Redundancy: 5.9 % / CC1/2: 0.999 / Net I/σ(I): 12.34
Reflection shellResolution: 1.12→1.162 Å / Num. unique obs: 7617 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→42.53 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.08 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14619 5111 4.9 %RANDOM
Rwork0.12301 ---
obs0.12413 98954 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.372 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å2-0 Å2
2---0.37 Å20 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.12→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 43 306 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132329
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172194
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.6643187
X-RAY DIFFRACTIONr_angle_other_deg1.6531.5935120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7495314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14622.768112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71615414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3691514
X-RAY DIFFRACTIONr_chiral_restr0.1130.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212712
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021474
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3991.3081185
X-RAY DIFFRACTIONr_mcbond_other1.3441.3051184
X-RAY DIFFRACTIONr_mcangle_it1.4921.9661518
X-RAY DIFFRACTIONr_mcangle_other1.5051.9681519
X-RAY DIFFRACTIONr_scbond_it2.5781.6431143
X-RAY DIFFRACTIONr_scbond_other2.5221.6241139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1312.321662
X-RAY DIFFRACTIONr_long_range_B_refined3.03917.7852723
X-RAY DIFFRACTIONr_long_range_B_other2.83516.9922650
X-RAY DIFFRACTIONr_rigid_bond_restr2.92834522
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.122→1.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 252 -
Rwork0.389 4696 -
obs--62.68 %

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