9M7M
Crystal structure of human pseudouridine 5'-monophosphate phosphatase (hHDHD1A) complexed with pseudouridine
Summary for 9M7M
| Entry DOI | 10.2210/pdb9m7m/pdb |
| Descriptor | Pseudouridine-5'-phosphatase, MAGNESIUM ION, 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione, ... (4 entities in total) |
| Functional Keywords | pseudouridine monophosphate phosphatase, had phosphatase, cofactor, pseudouridine, rna binding protein |
| Biological source | Homo sapiens (human) |
| Total number of polymer chains | 1 |
| Total formula weight | 25343.46 |
| Authors | |
| Primary citation | Seo, S.,Kim, M.,Rhee, S. Structural and functional insights into the substrate specificity of the pseudouridine monophosphate phosphatase HDHD1A. J.Biol.Chem., 301:110257-110257, 2025 Cited by 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-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. PubMed: 40409548DOI: 10.1016/j.jbc.2025.110257 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.26 Å) |
Structure validation
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