TY - JOUR
T1 - Analysis of ancient sequence motifs in the H+-PPase family
AU - Hedlund, Joel
AU - Cantoni, Roberto
AU - Baltscheffsky, Margareta
AU - Baltscheffsky, Herrick
AU - Persson, Bengt
PY - 2006/11
Y1 - 2006/11
N2 - The unique family of membrane-bound proton-pumping inorganic pyrophosphatases, involving pyrophosphate as the alternative to ATP, was investigated by characterizing 166 members of the UniProtKB/Swiss-Prot + UniProtKB/TrEMBL databases and available completed genomes, using sequence comparisons and a hidden Markov model based upon a conserved 57-residue region in the loop between transmembrane segments 5 and 6. The hidden Markov model was also used to search the approximately one million sequences recently reported from a large-scale sequencing project of organisms in the Sargasso Sea, resulting in additional 164 partial pyrophosphatase sequences. The strongly conserved 57-residue region was found to contain two nonapeptidyl sequences, mainly consisting of the four 'very early' proteinaceous amino acid residues Gly, Ala, Val and Asp, compatible with an ancient origin of the inorganic pyrophosphatases. The nonapeptide patterns have charged amino acid residues at positions 1, 5 and 9, are apparent binding sites for the substrate and parts of the active site, and were shown to be so specific for these enzymes that they can be used for functional assignments of unannotated genomes.
AB - The unique family of membrane-bound proton-pumping inorganic pyrophosphatases, involving pyrophosphate as the alternative to ATP, was investigated by characterizing 166 members of the UniProtKB/Swiss-Prot + UniProtKB/TrEMBL databases and available completed genomes, using sequence comparisons and a hidden Markov model based upon a conserved 57-residue region in the loop between transmembrane segments 5 and 6. The hidden Markov model was also used to search the approximately one million sequences recently reported from a large-scale sequencing project of organisms in the Sargasso Sea, resulting in additional 164 partial pyrophosphatase sequences. The strongly conserved 57-residue region was found to contain two nonapeptidyl sequences, mainly consisting of the four 'very early' proteinaceous amino acid residues Gly, Ala, Val and Asp, compatible with an ancient origin of the inorganic pyrophosphatases. The nonapeptide patterns have charged amino acid residues at positions 1, 5 and 9, are apparent binding sites for the substrate and parts of the active site, and were shown to be so specific for these enzymes that they can be used for functional assignments of unannotated genomes.
KW - Bioinformatics
KW - Hidden Markov models
KW - Molecular evolution
KW - Proteinaceous amino acids
KW - Pyrophosphatase
UR - http://www.scopus.com/inward/record.url?scp=33750539554&partnerID=8YFLogxK
UR - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=pure_univeritat_ramon_llull&SrcAuth=WosAPI&KeyUT=WOS:000241674500016&DestLinkType=FullRecord&DestApp=WOS_CPL
U2 - 10.1111/j.1742-4658.2006.05514.x
DO - 10.1111/j.1742-4658.2006.05514.x
M3 - Article
C2 - 17054711
AN - SCOPUS:33750539554
SN - 1742-464X
VL - 273
SP - 5183
EP - 5193
JO - FEBS Journal
JF - FEBS Journal
IS - 22
ER -