2IVN | pdb_00002ivn

Structure of UP1 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.224 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

An Archaeal Orthologue of the Universal Protein Kae1 is an Iron Metalloprotein which Exhibits Atypical DNA-Binding Properties and Apurinic-Endonuclease Activity in Vitro.

Hecker, A.Leulliot, N.Gadelle, D.Graille, M.Justome, A.Dorlet, P.Brochier, C.Quevillon-Cheruel, S.Le Cam, E.Van Tilbeurgh, H.Forterre, P.

(2007) Nucleic Acids Res 35: 6042

  • DOI: https://doi.org/10.1093/nar/gkm554
  • Primary Citation Related Structures: 
    2IVN, 2IVO, 2IVP

  • PubMed Abstract: 

    The Kae1 (Kinase-associated endopeptidase 1) protein is a member of the recently identified transcription complex EKC and telomeres maintenance complex KEOPS in yeast. Kae1 homologues are encoded by all sequenced genomes in the three domains of life. Although annotated as putative endopeptidases, the actual functions of these universal proteins are unknown. Here we show that the purified Kae1 protein (Pa-Kae1) from Pyrococcus abyssi is an iron-protein with a novel type of ATP-binding site. Surprisingly, this protein did not exhibit endopeptidase activity in vitro but binds cooperatively to single and double-stranded DNA and induces unusual DNA conformational change. Furthermore, Pa-Kae1 exhibits a class I apurinic (AP)-endonuclease activity (AP-lyase). Both DNA binding and AP-endonuclease activity are inhibited by ATP. Kae1 is thus a novel and atypical universal DNA interacting protein whose importance could rival those of RecA (RadA/Rad51) in the maintenance of genome integrity in all living cells.


  • Organizational Affiliation
    • Institut de Génétique et Microbiologie, Univ. Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France.

Macromolecule Content 

  • Total Structure Weight: 36.87 kDa 
  • Atom Count: 2,740 
  • Modeled Residue Count: 325 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-SIALOGLYCOPROTEIN ENDOPEPTIDASE330Pyrococcus abyssiMutation(s): 0 
EC: 3.4.24.57 (PDB Primary Data), 2.3.1.234 (UniProt)
UniProt
Find proteins for Q9UXT7 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UXT7 
Go to UniProtKB:  Q9UXT7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UXT7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.224 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.933α = 90
b = 69.868β = 90
c = 75.723γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other