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The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.

Ciccarelli FD, Izaurralde E, Bork P - BMC Bioinformatics (2003)

Bottom Line: We identified a new module, the PAM domain (PCI/PINT associated module), present in single subunits of well characterized multiprotein complexes, like the regulatory lid of the 26S proteasome, the COP-9 signalosome and the Sac3-Thp1 complex.This module is an around 200 residue long domain with a predicted TPR-like all-alpha-helical fold.The occurrence of the PAM domain in specific subunits of multimeric protein complexes, together with the role of other all-alpha-helical folds in protein-protein interactions, suggest a function for this domain in mediating transient binding to diverse target proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory, Meyerhofstr, 1, 69012 Heidelberg, Germany. francesca.ciccarelli@embl.de

ABSTRACT

Background: Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence.

Results: We identified a new module, the PAM domain (PCI/PINT associated module), present in single subunits of well characterized multiprotein complexes, like the regulatory lid of the 26S proteasome, the COP-9 signalosome and the Sac3-Thp1 complex. This module is an around 200 residue long domain with a predicted TPR-like all-alpha-helical fold.

Conclusions: The occurrence of the PAM domain in specific subunits of multimeric protein complexes, together with the role of other all-alpha-helical folds in protein-protein interactions, suggest a function for this domain in mediating transient binding to diverse target proteins.

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Multiple sequence alignment of representative proteins containing the PAM domain. Of the original set, only sequences with less than 80% identity to each other are shown. The borders of the domain have been assigned taking into account the results of the sequence alignments from PSI-BLAST [17] and the structural alignments from 3D-Jury [23]. Sequences are grouped by phylogenetic relationships, as explained in the legend to Fig. 2. For each sequence, the species, the domain starting and ending residues and the database accession number are reported. The consensus in 70% of the sequences is below the alignment; h, l, p and + indicate hydrophobic, aliphatic, polar, and positive residues, respectively. Hydrophobic residues are highlighted in blue, aliphatic residues in cyan, polar residues in green, positive residues in red and other conserved residues in yellow. The secondary structure predictions using PHD [24], PsiPred [25] and SAM-T99 [26] are reported. For PHD, the upper cases indicate elements predicted with expected average accuracy >82%, and lower cases those predicted with expected average accuracy <82%. The consensus among the three methods is indicated in red. The secondary structure elements of the Sec17 3D structure (1QQE) [27], taken as a representative of the TPR-like structural superfamily, are shown as red cylinders (α-helices: α5–α13). Abbreviations: Ag; Anopheles gambiae; At: Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cs, Ciona savignyi; Dm, Drosophila melanogaster; Hs, Homo sapiens; Nc, Neurospora crassa; Nt: Nicotiana tabacum; Pf, Plasmodium falciparum; Py, Plasmodium yoelii; Sc, saccharomyces cerevisiae; Sp: Schizosaccharomices pombae; Tb, Trypanosoma brucei, Ec, Encephalitozoon cuniculi, H, helix.
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Figure 1: Multiple sequence alignment of representative proteins containing the PAM domain. Of the original set, only sequences with less than 80% identity to each other are shown. The borders of the domain have been assigned taking into account the results of the sequence alignments from PSI-BLAST [17] and the structural alignments from 3D-Jury [23]. Sequences are grouped by phylogenetic relationships, as explained in the legend to Fig. 2. For each sequence, the species, the domain starting and ending residues and the database accession number are reported. The consensus in 70% of the sequences is below the alignment; h, l, p and + indicate hydrophobic, aliphatic, polar, and positive residues, respectively. Hydrophobic residues are highlighted in blue, aliphatic residues in cyan, polar residues in green, positive residues in red and other conserved residues in yellow. The secondary structure predictions using PHD [24], PsiPred [25] and SAM-T99 [26] are reported. For PHD, the upper cases indicate elements predicted with expected average accuracy >82%, and lower cases those predicted with expected average accuracy <82%. The consensus among the three methods is indicated in red. The secondary structure elements of the Sec17 3D structure (1QQE) [27], taken as a representative of the TPR-like structural superfamily, are shown as red cylinders (α-helices: α5–α13). Abbreviations: Ag; Anopheles gambiae; At: Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cs, Ciona savignyi; Dm, Drosophila melanogaster; Hs, Homo sapiens; Nc, Neurospora crassa; Nt: Nicotiana tabacum; Pf, Plasmodium falciparum; Py, Plasmodium yoelii; Sc, saccharomyces cerevisiae; Sp: Schizosaccharomices pombae; Tb, Trypanosoma brucei, Ec, Encephalitozoon cuniculi, H, helix.

Mentions: In the course of the characterization of the different subgroups inside the PCI/PINT domain family, we identified a new region of sequence similarity associated with PCI/PINT domains, which we called PAM (for PCI/PINT associated module, Fig. 1). The starting point of our analysis was S. cerevisiae Thp1 (Q08231), a protein involved in transcription regulation and messenger RNA export [13-16]. In the C-terminal part of this protein (roughly from residue 300 to residue 430), a divergent PCI/PINT domain can be detected (Table 1, see Additional data), whilst in the N-terminal part no known modules are annotated. When using the entire protein to search the non-redundant protein database (nrdb), the region preceding the PCI/PINT domain showed significant similarity to uncharacterized proteins. We then restricted our search only to the N-terminal part of the sequence (residues 1 to 300). At the first iteration of PSI-BLAST [17], the putative orthologs of Thp1 in H. sapiens, D. melanogaster, A. gambiae and S. pombe were retrieved (Q9NUK6, Q9VTL1, EAA12851 and Q9Y820, respectively, with E-values from 10-05 to 10-03). After detecting uncharacterized proteins from A. thaliana (Q8GWE6, E = 10-15), N. crassa (EAA34699, E = 10-15 and EAA35198, E = 10-08), S. pombe (YE18_SCHPO, E = 10-11) and the CSN12 subunit of the yeast signalosome (YJ54_YEAST, E = 10-09), the search converged. A HMM profile derived from the non-redundant multiple alignment of the new region was used to refine the search in the nrdb with HMMer [18]. This analysis added the orthologs of the Rnp3 proteasome subunit and some uncharacterized proteins to the initial sequence-set. The final non-redundant multiple alignment of representative members of all the families is shown in Fig. 1. Interestingly, none of the elF3 subunits was detected.


The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.

Ciccarelli FD, Izaurralde E, Bork P - BMC Bioinformatics (2003)

Multiple sequence alignment of representative proteins containing the PAM domain. Of the original set, only sequences with less than 80% identity to each other are shown. The borders of the domain have been assigned taking into account the results of the sequence alignments from PSI-BLAST [17] and the structural alignments from 3D-Jury [23]. Sequences are grouped by phylogenetic relationships, as explained in the legend to Fig. 2. For each sequence, the species, the domain starting and ending residues and the database accession number are reported. The consensus in 70% of the sequences is below the alignment; h, l, p and + indicate hydrophobic, aliphatic, polar, and positive residues, respectively. Hydrophobic residues are highlighted in blue, aliphatic residues in cyan, polar residues in green, positive residues in red and other conserved residues in yellow. The secondary structure predictions using PHD [24], PsiPred [25] and SAM-T99 [26] are reported. For PHD, the upper cases indicate elements predicted with expected average accuracy >82%, and lower cases those predicted with expected average accuracy <82%. The consensus among the three methods is indicated in red. The secondary structure elements of the Sec17 3D structure (1QQE) [27], taken as a representative of the TPR-like structural superfamily, are shown as red cylinders (α-helices: α5–α13). Abbreviations: Ag; Anopheles gambiae; At: Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cs, Ciona savignyi; Dm, Drosophila melanogaster; Hs, Homo sapiens; Nc, Neurospora crassa; Nt: Nicotiana tabacum; Pf, Plasmodium falciparum; Py, Plasmodium yoelii; Sc, saccharomyces cerevisiae; Sp: Schizosaccharomices pombae; Tb, Trypanosoma brucei, Ec, Encephalitozoon cuniculi, H, helix.
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Figure 1: Multiple sequence alignment of representative proteins containing the PAM domain. Of the original set, only sequences with less than 80% identity to each other are shown. The borders of the domain have been assigned taking into account the results of the sequence alignments from PSI-BLAST [17] and the structural alignments from 3D-Jury [23]. Sequences are grouped by phylogenetic relationships, as explained in the legend to Fig. 2. For each sequence, the species, the domain starting and ending residues and the database accession number are reported. The consensus in 70% of the sequences is below the alignment; h, l, p and + indicate hydrophobic, aliphatic, polar, and positive residues, respectively. Hydrophobic residues are highlighted in blue, aliphatic residues in cyan, polar residues in green, positive residues in red and other conserved residues in yellow. The secondary structure predictions using PHD [24], PsiPred [25] and SAM-T99 [26] are reported. For PHD, the upper cases indicate elements predicted with expected average accuracy >82%, and lower cases those predicted with expected average accuracy <82%. The consensus among the three methods is indicated in red. The secondary structure elements of the Sec17 3D structure (1QQE) [27], taken as a representative of the TPR-like structural superfamily, are shown as red cylinders (α-helices: α5–α13). Abbreviations: Ag; Anopheles gambiae; At: Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cs, Ciona savignyi; Dm, Drosophila melanogaster; Hs, Homo sapiens; Nc, Neurospora crassa; Nt: Nicotiana tabacum; Pf, Plasmodium falciparum; Py, Plasmodium yoelii; Sc, saccharomyces cerevisiae; Sp: Schizosaccharomices pombae; Tb, Trypanosoma brucei, Ec, Encephalitozoon cuniculi, H, helix.
Mentions: In the course of the characterization of the different subgroups inside the PCI/PINT domain family, we identified a new region of sequence similarity associated with PCI/PINT domains, which we called PAM (for PCI/PINT associated module, Fig. 1). The starting point of our analysis was S. cerevisiae Thp1 (Q08231), a protein involved in transcription regulation and messenger RNA export [13-16]. In the C-terminal part of this protein (roughly from residue 300 to residue 430), a divergent PCI/PINT domain can be detected (Table 1, see Additional data), whilst in the N-terminal part no known modules are annotated. When using the entire protein to search the non-redundant protein database (nrdb), the region preceding the PCI/PINT domain showed significant similarity to uncharacterized proteins. We then restricted our search only to the N-terminal part of the sequence (residues 1 to 300). At the first iteration of PSI-BLAST [17], the putative orthologs of Thp1 in H. sapiens, D. melanogaster, A. gambiae and S. pombe were retrieved (Q9NUK6, Q9VTL1, EAA12851 and Q9Y820, respectively, with E-values from 10-05 to 10-03). After detecting uncharacterized proteins from A. thaliana (Q8GWE6, E = 10-15), N. crassa (EAA34699, E = 10-15 and EAA35198, E = 10-08), S. pombe (YE18_SCHPO, E = 10-11) and the CSN12 subunit of the yeast signalosome (YJ54_YEAST, E = 10-09), the search converged. A HMM profile derived from the non-redundant multiple alignment of the new region was used to refine the search in the nrdb with HMMer [18]. This analysis added the orthologs of the Rnp3 proteasome subunit and some uncharacterized proteins to the initial sequence-set. The final non-redundant multiple alignment of representative members of all the families is shown in Fig. 1. Interestingly, none of the elF3 subunits was detected.

Bottom Line: We identified a new module, the PAM domain (PCI/PINT associated module), present in single subunits of well characterized multiprotein complexes, like the regulatory lid of the 26S proteasome, the COP-9 signalosome and the Sac3-Thp1 complex.This module is an around 200 residue long domain with a predicted TPR-like all-alpha-helical fold.The occurrence of the PAM domain in specific subunits of multimeric protein complexes, together with the role of other all-alpha-helical folds in protein-protein interactions, suggest a function for this domain in mediating transient binding to diverse target proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory, Meyerhofstr, 1, 69012 Heidelberg, Germany. francesca.ciccarelli@embl.de

ABSTRACT

Background: Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence.

Results: We identified a new module, the PAM domain (PCI/PINT associated module), present in single subunits of well characterized multiprotein complexes, like the regulatory lid of the 26S proteasome, the COP-9 signalosome and the Sac3-Thp1 complex. This module is an around 200 residue long domain with a predicted TPR-like all-alpha-helical fold.

Conclusions: The occurrence of the PAM domain in specific subunits of multimeric protein complexes, together with the role of other all-alpha-helical folds in protein-protein interactions, suggest a function for this domain in mediating transient binding to diverse target proteins.

Show MeSH