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Science 7 March 1997:
Vol. 275. no. 5305, pp. 1489 - 1490
DOI: 10.1126/science.275.5305.1489
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Technical Comments
Evidence for a Family of Archaeal ATPases
The analysis by Carol J. Bult et
al. of the Methanococcus jannaschii genome included
families of paralogous proteins that did not seem to have counterparts
in the current sequence databases (1). The largest of such
families consists of 13 chromosomal and three plasmid-encoded proteins,
which were found to be highly similar to one another [figure 6 in
(1)], but did not show statistically significant similarity
to any proteins, thus escaping functional prediction. Our inspection of
the alignment, however, indicates that two of the conserved sequence
blocks correspond to well-characterized functional motifs: namely, the
phosphate-binding P-loop and the Mg2+-binding site that are
conserved in a vast variety of ATPases and GTPases (Fig.
1 and 2-4). Even though most commonly used
methods for database search such as BLASTP (5) showed only
marginally significant similarity to several ATPases, a new version of
the BLASTP program that constructs local alignments with gaps
(6) indicated a probability of matching by chance between
10 4 and 106 for some of the proteins in the
new archaeal family and bacterial DnaA proteins; the conservation was
particularly notable in the two ATPase motifs (Fig. 1). Thus, even
though these 16 proteins comprise a novel family that is so far
represented only in archaea, they appear to belong to a known broad
class of proteins, and we predict that they possess ATPase activity.
Fig. 1.
Alignment of the three conserved motifs in the novel
family of putative archaeal ATPases. Alignment was constructed using the MACAW program (11). Consensus shows amino acid residues conserved in all of the 16 aligned sequences; h indicates a bulky hydrophobic residue (I, L, V, M, F, Y, W); $ indicates serine or
threonine. Distances from the protein N-termini and distances between
the alignment blocks are indicated by numbers. Fragments of the
Bacillus subtilis DnaA protein and Escherichia
coli Fur protein are shown for comparison. Two ATPase motifs and
the conserved histidine and cysteine residues in the predicted
metal-binding site are shown by reversed type. ATPase motif consensus
is from (4); <hhh> indicates that three out of five
residues preceding the first invariant G in the P-loop and the first D
in the Mg2+-binding motif are bulky and hydrophobic. In
addition to the proteins shown, open reading frames MJ0819, MJ0820, and
MJ0821 appear to represent remnants of a disrupted gene coding for a
putative ATPase of the same family.
[View Larger Version of this Image (49K GIF file)]
Screening of the nonredundant protein sequence database
at the National Center for Biotechnology Information (National
Institutes of Health, Bethesda, MD), with a bipartite pattern
representing the specific forms of the two ATPase motifs
conserved in the M. jannaschii family--namely,
hhhhGx4- GK[TS]xnhhhhD[DE] (h indicates a
bulky hydrophobic residue), selected 271 proteins, all of which are
either known to possess ATPase activity or are highly similar to
ATPases. In addition to DnaA, this list includes a number of members of the so-called AAA ATPase family (7); the
similarity between these proteins and DnaA has been noted before
(4). Many of the AAA family proteins possess chaperone-like
activity and, in particular, are involved in ATP-dependent proteolysis; examples include bacterial proteins ClpA, ClpB, ClpX, FtsH, and HslU;
proteasome components; and yeast HSP78 (7). Members of the
novel archaeal protein family could also perform chaperone-like functions. This is particularly plausible, because M. jannaschii does not encode several molecular chaperones that are
ubiquitous and highly conserved in bacteria and eukaryotes--namely,
members of the HSP70, HSP90, and HSP40 families. It remains to be seen how typical is this situation in archaea.
Finally, the family of putative ATPases contains a third strikingly
conserved motif with two invariant histidines and one invariant
cysteine (Fig. 1). Even though this motif did not show statistically
significant similarity to any proteins in the database, this may be a
specific metal-binding site, and some resemblance of the divalent
cation-binding motif in bacterial Fur proteins that are metal-dependent
transcription regulators (8) could be detected (Fig. 1). Two
observations seem relevant: (i) One of the chaperone ATPases, FtsH,
contains a metal-binding motif conserved in its bacterial and
eukaryotic homologs and is a Zn-dependent protease (9). (ii)
Methanococcus jannaschii encodes at least two other putative
ATPases, namely, the predicted proteins MJ0578 and MJ0579 that also
contain a metal-binding domain, in these cases a ferredoxin-like domain
(10).
Thus, analysis of conserved motifs and application of
additional methods for sequence database search yields specific
functional predictions for archaeal proteins that initially appeared to
comprise a unique family. There is little doubt that further
exploration of the M. jannaschii genome sequence will bring
more interesting findings.
Eugene V. Koonin
National Center for Biotechnology Information
National Library
of Medicine
National Institutes of Health
Bethesda, MD 20894, USA
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12 September
1996; accepted 16 January 1997
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