8K05

Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- sulfate bound holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Literature

Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.

Lee, J.Kim, S.H.Rhee, S.

(2024) RNA Biol 21: 1-10

  • DOI: https://doi.org/10.1080/15476286.2023.2293340
  • Primary Citation of Related Structures:  
    8K05, 8K06, 8K07

  • PubMed Abstract: 

    Pseudouridine is a noncanonical C -nucleoside containing a C-C glycosidic linkage between uracil and ribose. In the two-step degradation of pseudouridine, pseudouridine 5'-monophosphate glycosylase (PUMY) is responsible for the second step and catalyses the cleavage of the C-C glycosidic bond in pseudouridine 5'-monophosphate (ΨMP) into uridine and ribose 5'-phosphate, which are recycled via other metabolic pathways. Structural features of Escherichia coli PUMY have been reported, but the details of the substrate specificity of ΨMP were unknown. Here, we present three crystal structures of Arabidopsis thaliana PUMY in different ligation states and a kinetic analysis of ΨMP degradation. The results indicate that Thr149 and Asn308, which are conserved in the PUMY family, are structural determinants for recognizing the nucleobase of ΨMP. The distinct binding modes of ΨMP and ribose 5'-phosphate also suggest that the nucleobase, rather than the phosphate group, of ΨMP dictates the substrate-binding mode. An open-to-close transition of the active site is essential for catalysis, which is mediated by two α-helices, α11 and α12, near the active site. Mutational analysis validates the proposed roles of the active site residues in catalysis. Our structural and functional analyses provide further insight into the enzymatic features of PUMY towards ΨMP.


  • 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'-phosphate glycosidase340Arabidopsis thalianaMutation(s): 0 
Gene Names: PUMYAt1g50510F11F12.14
EC: 4.2.1.70
UniProt
Find proteins for Q84K35 (Arabidopsis thaliana)
Explore Q84K35 
Go to UniProtKB:  Q84K35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84K35
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.126α = 90
b = 121.126β = 90
c = 121.126γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1A2C2092118

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release