PDBsum entry 1v8o

Structural genomics, unknown function

PDB id: 1v8o

Contents

Protein chains

(+ 2 more) 132 a.a. *

Metals

_CL ×4

Waters ×66

* Residue conservation analysis

PDB id:

1v8o

Name:

Structural genomics, unknown function

Title:

Crystal structure of pae2754 from pyrobaculum aerophilum

Structure:

Hypothetical protein pae2754. Chain: a, b, c, d, e, f, g, h. Engineered: yes. Mutation: yes

Source:

Pyrobaculum aerophilum. Organism_taxid: 13773. Gene: pae2754. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.226 R-free: 0.279

Authors:

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

Key ref:

V.L.Arcus et al. (2004). Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease. J Biol Chem, 279, 16471-16478. PubMed id: 14734548 DOI: 10.1074/jbc.M313833200

Date:

12-Jan-04 Release date: 10-Feb-04

Protein chains

Q8ZUJ3  (VAPC9_PYRAE) -  Exonuclease VapC9 from Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)

Seq: 133 a.a.

Struc: 132 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

DOI no: 10.1074/jbc.M313833200

J Biol Chem 279:16471-16478 (2004)

PubMed id: 14734548

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

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

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.

Selected figure(s)

Figure 2.
FIG. 2. Oligomeric state for PAE2754 showing conserved residues. A, view of the dimer showing the residues that are conserved across COG4113 (also shown in the alignment in Fig. 3). For chain A, three of the residues are labeled with their one-letter amino acid code. B, surface depiction (in the same orientation as A) of the PAE2754 dimer showing electrostatic charges at the surface using GRASP. C, orthogonal views of the tetramer surface showing the tunnel inside which the putative active site resides. This figure was drawn using PyMol (38) and GRASP (39).

Figure 5.
FIG. 5. In vitro exonuclease activity of PAE2754. A polyacrylamide/urea denaturing gel showing DNA stained by ethidium bromide (see text). Lane A shows the 54-bp oligonucleotide alone. Lanes B-G show 1-5- and 19-h incubations, respectively, of annealed oligonucleotides (54 + 18 bp) with PAE2754 and MgCl[2] at 37 °C. Lane H shows a 19-h incubation of annealed oligonucleotides (54 + 18 bp) with PAE2754 at 37 °C in the absence of MgCl[2].

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 16471-16478) copyright 2004.

Figures were selected by an automated process.