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- PDB-9w5a: The structure of dUTPase in complex with dUTP from Methanosarcina... -

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Basic information

Entry
Database: PDB / ID: 9w5a
TitleThe structure of dUTPase in complex with dUTP from Methanosarcina mazei
ComponentsProbable deoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / Archaea / dUTPase / trimeric enzyme / crystal structure / subdomain I / evolutionary divergence
Function / homology
Function and homology information


dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase, archaeal / dCTP deaminase / dCTP deaminase-like / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
DEOXYURIDINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Probable deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å
AuthorsChen, S.C. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)NSTC114-2113-M-002-009-MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural and functional insights into an archaeal dUTPase reveal a subdomain-mediated mechanism for substrate recognition and evolutionary adaptation.
Authors: Chen, S.C. / Chou, C.C. / Chen, W.M. / Sheu, S.Y. / Huang, L.W. / Huang, C.H. / Chang, S.C. / Kuo, C.H. / Hsu, C.H.
History
DepositionAug 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Probable deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Probable deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8597
Polymers61,3603
Non-polymers1,4994
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-63 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.971, 81.971, 81.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Probable deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 20453.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: dut, MM_1628 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PWG1, dUTP diphosphatase
#2: Chemical ChemComp-DUT / DEOXYURIDINE-5'-TRIPHOSPHATE


Mass: 468.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.26M potassium phosphate monobasic and 0.14M sodium phosphate dibasic, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 81018 / % possible obs: 99.7 % / Redundancy: 7.9 % / Biso Wilson estimate: 20.03 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 48.3
Reflection shellResolution: 1.53→1.58 Å / Num. unique obs: 8082 / Rpim(I) all: 0.555

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.53→27.31 Å / SU ML: 0.167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2038 1982 2.45 %
Rwork0.1743 78908 -
obs0.175 80890 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.55 Å2
Refinement stepCycle: LAST / Resolution: 1.53→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 89 495 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733904
X-RAY DIFFRACTIONf_angle_d1.02935332
X-RAY DIFFRACTIONf_chiral_restr0.0603605
X-RAY DIFFRACTIONf_plane_restr0.008676
X-RAY DIFFRACTIONf_dihedral_angle_d14.19011495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.3031420.24555622X-RAY DIFFRACTION99.45
1.57-1.610.23411300.2175614X-RAY DIFFRACTION99.69
1.61-1.660.2081490.20365624X-RAY DIFFRACTION99.72
1.66-1.710.21551450.19645619X-RAY DIFFRACTION99.88
1.71-1.770.22311390.19095630X-RAY DIFFRACTION99.91
1.77-1.850.23121520.19025625X-RAY DIFFRACTION99.95
1.85-1.930.19221450.1845660X-RAY DIFFRACTION99.95
1.93-2.030.17971310.17955652X-RAY DIFFRACTION99.98
2.03-2.160.20461370.17245665X-RAY DIFFRACTION100
2.16-2.320.18871480.17515626X-RAY DIFFRACTION99.98
2.32-2.560.21831410.18455657X-RAY DIFFRACTION100
2.56-2.930.2411460.1885663X-RAY DIFFRACTION99.97
2.93-3.690.20481320.16355671X-RAY DIFFRACTION99.67
3.69-27.310.17371450.15135580X-RAY DIFFRACTION96.58

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