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- PDB-9m7m: Crystal structure of human pseudouridine 5'-monophosphate phospha... -

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Basic information

Entry
Database: PDB / ID: 9m7m
TitleCrystal structure of human pseudouridine 5'-monophosphate phosphatase (hHDHD1A) complexed with pseudouridine
ComponentsPseudouridine-5'-phosphatase
KeywordsRNA BINDING PROTEIN / pseudouridine monophosphate phosphatase / HAD phosphatase / cofactor / pseudouridine
Function / homology
Function and homology information


pseudouridine 5'-phosphatase / pseudouridine 5'-phosphatase activity / Pyrimidine salvage / nucleotide metabolic process / phosphatase activity / metal ion binding / cytosol
Similarity search - Function
Phosphatase Gpp1/Gpp2-like / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Chem-FJF / Pseudouridine-5'-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å
AuthorsSeo, S. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural and functional insights in the substrate specificity of the pseudouridine monophosphate phosphatase HDHD1A.
Authors: Seo, S. / Kim, M. / Rhee, S.
History
DepositionMar 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudouridine-5'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3433
Polymers25,0751
Non-polymers2692
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.620, 61.090, 68.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-615-

HOH

31A-618-

HOH

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Components

#1: Protein Pseudouridine-5'-phosphatase / Haloacid dehalogenase-like hydrolase domain-containing protein 1 / Haloacid dehalogenase-like ...Haloacid dehalogenase-like hydrolase domain-containing protein 1 / Haloacid dehalogenase-like hydrolase domain-containing protein 1A / Protein GS1 / Pseudouridine-5'-monophosphatase / 5'-PsiMPase


Mass: 25074.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUDP, DXF68S1E, FAM16AX, GS1, HDHD1, HDHD1A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08623, pseudouridine 5'-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FJF / 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl (pH 8.5), 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.26→30 Å / Num. obs: 107923 / % possible obs: 95.6 % / Redundancy: 12.53 % / CC1/2: 1 / Net I/σ(I): 18.89
Reflection shellResolution: 1.26→1.31 Å / Num. unique obs: 6012 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSv20230630data reduction
XDSv20230630data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 1.26→29.792 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 3836 3.55 %
Rwork0.1836 --
obs0.1845 107923 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→29.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 18 300 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161819
X-RAY DIFFRACTIONf_angle_d1.5512470
X-RAY DIFFRACTIONf_dihedral_angle_d11.635675
X-RAY DIFFRACTIONf_chiral_restr0.096282
X-RAY DIFFRACTIONf_plane_restr0.01318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2601-1.2760.33471380.30083756X-RAY DIFFRACTION93
1.276-1.29280.32691390.28953759X-RAY DIFFRACTION94
1.2928-1.31050.32211430.29163834X-RAY DIFFRACTION95
1.3105-1.32920.30451390.28323817X-RAY DIFFRACTION95
1.3292-1.34910.29191400.27263851X-RAY DIFFRACTION96
1.3491-1.37020.28521360.27013780X-RAY DIFFRACTION95
1.3702-1.39260.36941410.26913798X-RAY DIFFRACTION95
1.3926-1.41660.25661400.27143854X-RAY DIFFRACTION96
1.4166-1.44240.26241420.25333821X-RAY DIFFRACTION95
1.4424-1.47010.26911390.25343762X-RAY DIFFRACTION95
1.4701-1.50010.27961440.23623825X-RAY DIFFRACTION94
1.5001-1.53280.24771380.2343714X-RAY DIFFRACTION93
1.5328-1.56840.22921430.22353859X-RAY DIFFRACTION94
1.5684-1.60760.23541390.21653759X-RAY DIFFRACTION94
1.6076-1.65110.28631350.22933748X-RAY DIFFRACTION94
1.6511-1.69970.25481390.2183795X-RAY DIFFRACTION94
1.6997-1.75450.26831380.20943777X-RAY DIFFRACTION94
1.7545-1.81720.20191450.19443882X-RAY DIFFRACTION95
1.8172-1.890.20631430.18393871X-RAY DIFFRACTION97
1.89-1.9760.20241450.17753902X-RAY DIFFRACTION97
1.976-2.08010.23621430.17763929X-RAY DIFFRACTION98
2.0801-2.21040.21151440.16843958X-RAY DIFFRACTION99
2.2104-2.3810.21581480.16164001X-RAY DIFFRACTION99
2.381-2.62050.17511490.15883992X-RAY DIFFRACTION99
2.6205-2.99940.18041520.17054009X-RAY DIFFRACTION100
2.9994-3.77770.17281490.15274027X-RAY DIFFRACTION100
3.7777-29.7920.15051450.13914007X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.003 Å / Origin y: 16.0201 Å / Origin z: 11.5378 Å
111213212223313233
T0.0569 Å2-0.0169 Å2-0.0135 Å2-0.0295 Å20.0166 Å2--0.057 Å2
L0.7028 °20.0117 °20.6489 °2-0.4852 °20.1282 °2--1.4542 °2
S0.0752 Å °-0.0937 Å °-0.0587 Å °0.0475 Å °-0.018 Å °-0.0281 Å °0.0783 Å °-0.0235 Å °0.0301 Å °
Refinement TLS groupSelection details: all

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