Sequence motifs
Two sequence motifs were reported previously in 46 for
the PURase from Pseudomonoas chlororaphis , PueA (Table
3 ). The occurrence of the serine hydrolase motif (GXSXG) and the
secretion signal sequence motif (GGXGXDXXX) were confirmed for the vast
majority of all 2054 sequence entries in a multiple sequence alignment
for superfamily 11 of the LED. Most PURase homologues from superfamily
11 have a GHSLG motif flanking the catalytic serine and secretion motif
GGKGNDYLE. For sequences from superfamily 11 in the LED, the catalytic
triad is formed by serine, aspartate, and histidine. In addition, most
sequences in superfamily 11 (2039 out of 2054) matched the profile HMM
for a RTX calcium-binding nonapeptide repeat (PFAM PF00353), which
supports the previous suggestion of a Type I secretion system for
protein translocation 47.
Prominent amino acid positions in superfamily 13, which comprises
homologues of the PURase PudA from Delftia acidovorans , include
the GXSXG serine hydrolase motif, a catalytic triad of serine,
aspartate, and histidine, and a putative PUR binding region at PudA
positions 347 to 395 48. Many of these positions were
found to be conserved within the sequences of superfamily 13
(Table 4 ). Most PURase homologues from superfamily 13 have the
motif GES AG flanking the catalytic serine, the motif
VPX3G[ST]X2DE at the
catalytic glutamate, and the motif
AXH X3[LI]XY flanking the catalytic
histidine. In addition, several positions in the putative PUR binding
region were found to be conserved, including mostly hydrophobic amino
acids (Table S8 ).