1ZTH

Crystal Structure of A.fulgidus Rio1 serine protein kinase bound to ADP and Manganese ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Structure and activity of the atypical serine kinase Rio1.

Laronde-Leblanc, N.Guszczynski, T.Copeland, T.Wlodawer, A.

(2005) FEBS J 272: 3698-3713

  • DOI: https://doi.org/10.1111/j.1742-4658.2005.04796.x
  • Primary Citation of Related Structures:  
    1ZP9, 1ZTF, 1ZTH

  • PubMed Abstract: 

    Rio1 is the founding member of the RIO family of atypical serine kinases that are universally present in all organisms from archaea to mammals. Activity of Rio1 was shown to be absolutely essential in Saccharomyces cerevisiae for the processing of 18S ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. We determined high-resolution crystal structures of Archaeoglobus fulgidus Rio1 in the presence and absence of bound nucleotides. Crystallization of Rio1 in the presence of ATP or ADP and manganese ions demonstrated major conformational changes in the active site, compared with the uncomplexed protein. Comparisons of the structure of Rio1 with the previously determined structure of the Rio2 kinase defined the minimal RIO domain and the distinct features of the RIO subfamilies. We report here that Ser108 represents the sole autophosphorylation site of A. fulgidus Rio1 and have therefore established its putative peptide substrate. In addition, we show that a mutant enzyme that cannot be autophosphorylated can still phosphorylate an inactive form of Rio1, as well as a number of typical kinase substrates.


  • Organizational Affiliation

    Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, NCI-Frederick, MD 21702-1201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rio1 serine protein kinase
A, B, C, D
258Archaeoglobus fulgidusMutation(s): 11 
Gene Names: Rio1
EC: 2.7.11.1
UniProt
Find proteins for O28471 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28471 
Go to UniProtKB:  O28471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28471
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.414α = 90
b = 80.084β = 90.17
c = 121.056γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection
  • Version 1.6: 2024-11-20
    Changes: Structure summary