9M7M | pdb_00009m7m

Crystal structure of human pseudouridine 5'-monophosphate phosphatase (hHDHD1A) complexed with pseudouridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 
    0.209 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

Structural and functional insights into the substrate specificity of the pseudouridine monophosphate phosphatase HDHD1A.

Seo, S.Kim, M.Rhee, S.

(2025) J Biological Chem 301: 110257-110257

  • DOI: https://doi.org/10.1016/j.jbc.2025.110257
  • Primary Citation of Related Structures:  
    9M7L, 9M7M

  • PubMed Abstract: 

    Pseudouridine (Ψ) is one of the most abundant RNA modifications. Following RNA degradation, Ψ nucleotides are dephosphorylated and catabolized into uracil and ribose 5'-phosphate via a two-step enzymatic reaction catalyzed by enzymes present in many bacteria and eukaryotes, but not in mammals. Malfunction of Ψ catabolism has adverse physiological effects in plants. In humans, the enzyme HDHD1A dephosphorylates pseudouridine 5'-monophosphate (ΨMP), and the resulting Ψ is excreted in the urine. In this study, we determined the crystal structures of human HDHD1A (hHDHD1A) complexed with Ψ. The structure of hHDHD1A consists of a catalytic domain with a Rossmann α/β-fold and a cap domain, with a magnesium ion at the junction of the two domains. Ψ is bound to the active site in an orientation where its nucleobase, uracil-Ψ, is surrounded by the cap domain residues, and the ribose moiety is located next to the Mg 2+ -binding site. The active site is composed mainly of hydrophobic residues, but two essential charged residues, Glu23 and Lys46, are present in the vicinity of uracil-Ψ. Glu23 interacts with the Ψ-specific N1 atom, while Lys46 interacts with the O2 atom of uracil-Ψ. Mutagenesis and kinetic analysis indicated that active site residues are involved in substrate binding and/or catalysis. In addition to Ψ-specific hydrophilic interactions, shape complementarity between ΨMP and the active site pocket is a key element underlying substrate specificity in hHDHD1A. This study provided structural and functional insights into the substrate specificity of hHDHD1A for ΨMP, highlighting both similarities and differences compared to other Ψ-recognizing enzymes.


  • Organizational Affiliation
    • Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudouridine-5'-phosphatase226Homo sapiensMutation(s): 0 
Gene Names: PUDPDXF68S1EFAM16AXGS1HDHD1HDHD1A
EC: 3.1.3.96
UniProt & NIH Common Fund Data Resources
Find proteins for Q08623 (Homo sapiens)
Explore Q08623 
Go to UniProtKB:  Q08623
PHAROS:  Q08623
GTEx:  ENSG00000130021 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08623
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FJF (Subject of Investigation/LOI)
Query on FJF

Download Ideal Coordinates CCD File 
C [auth A]5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione
C9 H12 N2 O6
PTJWIQPHWPFNBW-GBNDHIKLSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free:  0.209 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.62α = 90
b = 61.09β = 90
c = 68.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references