Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 36.87 kDa 
• Atom Count: 2740 
• Modelled Residue Count: 325 
• Deposited Residue Count: 330 
• Unique protein chains: 1

2IVN

Structure of UP1 protein

• PDB DOI: 10.2210/pdb2IVN/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-14 Released: 2007-07-31 
• Deposition Author(s): Hecker, A., Leulliot, N., Graille, M., Dorlet, P., Quevillon-Cheruel, S., Ulryck, N., Van Tilbeurgh, H., Forterre, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.224 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

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

• PubMed: 17766251 
• DOI: 10.1093/nar/gkm554
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-SIALOGLYCOPROTEIN ENDOPEPTIDASE	A	330	Pyrococcus abyssi	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.224 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.933	α = 90
b = 69.868	β = 90
c = 75.723	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-14 
• Released Date: 2007-07-31 
Deposition Author(s): Hecker, A., Leulliot, N., Graille, M., Dorlet, P., Quevillon-Cheruel, S., Ulryck, N., Van Tilbeurgh, H., Forterre, P.

Revision History  

• 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