Crystal structure of PAE2754 from Pyrobaculum aerophilum

Experimental Data Snapshot

  • Resolution: 2.52 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease

Arcus, V.L.Backbro, K.Roos, A.Daniel, E.L.Baker, E.N.

(2004) J Biol Chem 279: 16471-16478

  • DOI: https://doi.org/10.1074/jbc.M313833200
  • Primary Citation of Related Structures:  
    1V8O, 1V8P

  • PubMed Abstract: 

    Genome sequencing projects have focused attention on the problem of discovering the functions of protein domains that are widely distributed throughout living species but which are, as yet, largely uncharacterized. One such example is the PIN domain, found in eukaryotes, bacteria, and Archaea, and with suggested roles in signaling, RNase editing, and/or nucleotide binding. The first reported crystal structure of a PIN domain (open reading frame PAE2754, derived from the crenarchaeon, Pyrobaculum aerophilum) has been determined to 2.5 A resolution and is presented here. Mapping conserved residues from a multiple sequence alignment onto the structure identifies a putative active site. The discovery of distant structural homology with several exonucleases, including T4 phage RNase H and flap endonuclease (FEN1), further suggests a likely function for PIN domains as Mg2+-dependent exonucleases, a hypothesis that we have confirmed in vitro. The tetrameric structure of PAE2754, with the active sites inside a tunnel, suggests a mechanism for selective cleavage of single-stranded overhangs or flap structures. These results indicate likely DNA or RNA editing roles for prokaryotic PIN domains, which are strikingly numerous in thermophiles, and in organisms such as Mycobacterium tuberculosis. They also support previous hypotheses that eukaryotic PIN domains participate in RNAi and nonsense-mediated RNA degradation.

  • Organizational Affiliation

    School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand. v.arcus@auckland.ac.nz

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein PAE2754
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Pyrobaculum aerophilumMutation(s): 1 
Gene Names: PAE2754
Find proteins for Q8ZUJ3 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2))
Explore Q8ZUJ3 
Go to UniProtKB:  Q8ZUJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZUJ3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.52 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.56α = 90
b = 165.19β = 90
c = 203.35γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection