8JB3 | pdb_00008jb3

Structure and allosteric regulation of the inosine 5'-monophosphate-specific phosphatase ISN1 from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure, cooperativity and inhibition of the inosine 5'-monophosphate-specific phosphatase from Saccharomyces cerevisiae.

Byun, S.Park, C.Suh, J.Y.Witte, C.P.Rhee, S.

(2024) FEBS J 291: 1992-2008

  • DOI: https://doi.org/10.1111/febs.17093
  • Primary Citation of Related Structures:  
    8J6H, 8JB3

  • PubMed Abstract: 

    The nucleoside inosine is a main intermediate of purine nucleotide catabolism in Saccharomyces cerevisiae and is produced via the dephosphorylation of inosine monophosphate (IMP) by IMP-specific 5'-nucleotidase 1 (ISN1), which is present in many eukaryotic organisms. Upon transition of yeast from oxidative to fermentative growth, ISN1 is important for intermediate inosine accumulation as purine storage, but details of ISN1 regulation are unknown. We characterized structural and kinetic behavior of ISN1 from S. cerevisiae (ScISN1) and showed that tetrameric ScISN1 is negatively regulated by inosine and adenosine triphosphate (ATP). Regulation involves an inosine-binding allosteric site along with IMP-induced local and global conformational changes in the monomer and a tetrameric re-arrangement, respectively. A proposed interaction network propagates local conformational changes in the active site to the intersubunit interface, modulating the allosteric features of ScISN1. Via ATP and inosine, ScISN1 activity is likely fine-tuned to regulate IMP and inosine homeostasis. These regulatory and catalytic features of ScISN1 contrast with those of the structurally homologous ISN1 from Plasmodium falciparum, indicating that ISN1 enzymes may serve different biological purposes in different organisms.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase 1455Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: ISN1YOR155CO3548
EC: 3.1.3.99
UniProt
Find proteins for Q99312 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99312 
Go to UniProtKB:  Q99312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99312
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMP (Subject of Investigation/LOI)
Query on IMP

Download Ideal Coordinates CCD File 
D [auth A]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
NOS (Subject of Investigation/LOI)
Query on NOS

Download Ideal Coordinates CCD File 
B [auth A]INOSINE
C10 H12 N4 O5
UGQMRVRMYYASKQ-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.591α = 90
b = 180.591β = 90
c = 90.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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 Of2021R1A2C2092118
Ministry of Science, ICT and Future Planning (MSIP)Korea, Republic OfRS-2023-00207820

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Structure summary