MULTISPECIES: polyphosphate kinase 1 [Salmonella]
Protein Classification
polyphosphate kinase( domain architecture ID 11497495)
polyphosphate kinase catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP)
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| poly_P_kin | TIGR03705 | polyphosphate kinase 1; Members of this protein family are the enzyme polyphosphate kinase 1 ... |
7-680 | 0e+00 | ||||||||||
polyphosphate kinase 1; Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2. [Central intermediary metabolism, Phosphorus compounds] : Pssm-ID: 274734 [Multi-domain] Cd Length: 672 Bit Score: 952.35 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||||
| poly_P_kin | TIGR03705 | polyphosphate kinase 1; Members of this protein family are the enzyme polyphosphate kinase 1 ... |
7-680 | 0e+00 | ||||||||||
polyphosphate kinase 1; Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2. [Central intermediary metabolism, Phosphorus compounds] Pssm-ID: 274734 [Multi-domain] Cd Length: 672 Bit Score: 952.35 E-value: 0e+00
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| PRK05443 | PRK05443 | polyphosphate kinase; Provisional |
1-687 | 0e+00 | ||||||||||
polyphosphate kinase; Provisional Pssm-ID: 235469 [Multi-domain] Cd Length: 691 Bit Score: 942.63 E-value: 0e+00
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| Ppk | COG0855 | Polyphosphate kinase [Inorganic ion transport and metabolism]; |
3-686 | 0e+00 | ||||||||||
Polyphosphate kinase [Inorganic ion transport and metabolism]; Pssm-ID: 440616 [Multi-domain] Cd Length: 685 Bit Score: 941.39 E-value: 0e+00
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| PP_kinase_C_1 | pfam17941 | Polyphosphate kinase C-terminal domain 1; Polyphosphate kinase (Ppk) catalyzes the formation ... |
333-497 | 6.26e-108 | ||||||||||
Polyphosphate kinase C-terminal domain 1; Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains. Pssm-ID: 465578 Cd Length: 167 Bit Score: 323.91 E-value: 6.26e-108
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| PLDc_PPK1_C1 | cd09114 | Catalytic C-terminal domain, first repeat, of prokaryotic polyphosphate kinase 1 and similar ... |
331-492 | 2.70e-94 | ||||||||||
Catalytic C-terminal domain, first repeat, of prokaryotic polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, first repeat (C1 domain), of bacterial polyphosphate kinases 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. There is a second bacterial-type enzyme, PPK2, which is involved in the synthesis of poly P from GTP or ATP. PPK2 shows no sequence similarity to PPK1 and belongs to different superfamily. Pssm-ID: 197213 Cd Length: 162 Bit Score: 288.66 E-value: 2.70e-94
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| Name | Accession | Description | Interval | E-value | ||||||||||
| poly_P_kin | TIGR03705 | polyphosphate kinase 1; Members of this protein family are the enzyme polyphosphate kinase 1 ... |
7-680 | 0e+00 | ||||||||||
polyphosphate kinase 1; Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2. [Central intermediary metabolism, Phosphorus compounds] Pssm-ID: 274734 [Multi-domain] Cd Length: 672 Bit Score: 952.35 E-value: 0e+00
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| PRK05443 | PRK05443 | polyphosphate kinase; Provisional |
1-687 | 0e+00 | ||||||||||
polyphosphate kinase; Provisional Pssm-ID: 235469 [Multi-domain] Cd Length: 691 Bit Score: 942.63 E-value: 0e+00
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| Ppk | COG0855 | Polyphosphate kinase [Inorganic ion transport and metabolism]; |
3-686 | 0e+00 | ||||||||||
Polyphosphate kinase [Inorganic ion transport and metabolism]; Pssm-ID: 440616 [Multi-domain] Cd Length: 685 Bit Score: 941.39 E-value: 0e+00
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| PP_kinase_C_1 | pfam17941 | Polyphosphate kinase C-terminal domain 1; Polyphosphate kinase (Ppk) catalyzes the formation ... |
333-497 | 6.26e-108 | ||||||||||
Polyphosphate kinase C-terminal domain 1; Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains. Pssm-ID: 465578 Cd Length: 167 Bit Score: 323.91 E-value: 6.26e-108
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| PLDc_PPK1_C1 | cd09114 | Catalytic C-terminal domain, first repeat, of prokaryotic polyphosphate kinase 1 and similar ... |
331-492 | 2.70e-94 | ||||||||||
Catalytic C-terminal domain, first repeat, of prokaryotic polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, first repeat (C1 domain), of bacterial polyphosphate kinases 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. There is a second bacterial-type enzyme, PPK2, which is involved in the synthesis of poly P from GTP or ATP. PPK2 shows no sequence similarity to PPK1 and belongs to different superfamily. Pssm-ID: 197213 Cd Length: 162 Bit Score: 288.66 E-value: 2.70e-94
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| PLDc_EcPPK1_C1_like | cd09164 | Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and ... |
331-492 | 3.10e-93 | ||||||||||
Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, first repeat (C1 domain), of Escherichia coli polyphosphate kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. The prototype of this subfamily is Escherichia coli polyphosphate kinase (EcPPK), which forms a homotetramer in solution, and becomes a homodimer upon the binding of AMPPNP, a non-hydrolysable ATP analogue. Each EcPPK monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2)domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of EcPPK are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of EcPPK. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. Pssm-ID: 197261 Cd Length: 162 Bit Score: 285.65 E-value: 3.10e-93
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| PLDc_EcPPK1_C2_like | cd09167 | Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and ... |
500-664 | 1.54e-92 | ||||||||||
Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, second repeat (C2 domain), of Escherichia coli polyphosphate kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. The prototype of this subfamily is Escherichia coli polyphosphate kinase (EcPPK), which forms a homotetramer in solution, and becomes a homodimer upon the binding of AMPPNP, a non-hydrolysable ATP analogue. Each EcPPK monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2)domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of EcPPK are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of EcPPK. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. Pssm-ID: 197264 Cd Length: 165 Bit Score: 284.07 E-value: 1.54e-92
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| PLDc_PPK1_C2 | cd09115 | Catalytic C-terminal domain, second repeat, of prokaryotic polyphosphate kinase 1 and similar ... |
501-662 | 5.56e-90 | ||||||||||
Catalytic C-terminal domain, second repeat, of prokaryotic polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, second repeat (C2 domain), of bacterial polyphosphate kinases 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. There is a second bacterial-type enzyme, PPK2, which is involved in the synthesis of poly P from GTP or ATP. PPK2 shows no sequence similarity to PPK1 and belongs to different superfamily. Pssm-ID: 197214 Cd Length: 162 Bit Score: 277.51 E-value: 5.56e-90
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| PP_kinase_C | pfam13090 | Polyphosphate kinase C-terminal domain 2; Polyphosphate kinase (Ppk) catalyzes the formation ... |
503-674 | 4.31e-87 | ||||||||||
Polyphosphate kinase C-terminal domain 2; Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains. Pssm-ID: 463783 Cd Length: 172 Bit Score: 270.22 E-value: 4.31e-87
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| PLDc_PaPPK1_C1_like | cd09165 | Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 ... |
333-491 | 1.37e-83 | ||||||||||
Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, first repeat (C1 domain), of polyphosphate kinase (Poly P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1), and other similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PaPPK1 is the key enzyme responsible for the synthesis of Poly P in Pseudomonas aeruginosa. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. PaPPK1 shows high sequence homolog to Escherichia coli polyphosphate kinase (EcPPK), which contains four structural domains per chain: the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. The polyphosphate kinase from Dictyostelium discoideum (DdPPK1) shares similar structural features with EcPPK1 in the ATP-binding pocket and poly P tunnel, but has a unique N-terminal extension that may be responsible for its enzymatic activity, cellular localization, and physiological functions. In spite of the lack of sequence homology, the C1 and C2 domains of the family members are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. In some bacteria, such as Pseudomonas aeruginosa, a second enzyme, PPK2, which is involved in the alternative pathway of polyphosphate synthesis, has been found. It can catalyze the synthesis of poly P from GTP or ATP, with a preference for Mn2+ over Mg2+. PPK2 shows no sequence similarity to PPK1 and belongs to a different superfamily. Pssm-ID: 197262 Cd Length: 164 Bit Score: 260.97 E-value: 1.37e-83
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| PLDc_PaPPK1_C2_like | cd09168 | Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 ... |
500-652 | 1.19e-74 | ||||||||||
Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Catalytic C-terminal domain, second repeat (C2 domain), of polyphosphate kinase (Poly P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1), and other similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PaPPK1 is the key enzyme responsible for the synthesis of Poly P in Pseudomonas aeruginosa. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. PaPPK1 shows high sequence homolog to Escherichia coli polyphosphate kinase (EcPPK), which contains four structural domains per chain: the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. The polyphosphate kinase from Dictyostelium discoideum (DdPPK1) shares similar structural features with EcPPK1 in the ATP-binding pocket and poly P tunnel, but has a unique N-terminal extension that may be responsible for its enzymatic activity, cellular localization, and physiological functions. In spite of the lack of sequence homology, the C1 and C2 domains of the family members are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. In some bacteria, such as Pseudomonas aeruginosa, a second enzyme, PPK2, which is involved in the alternative pathway of polyphosphate synthesis, has been found. It can catalyze the synthesis of poly P from GTP or ATP, with a preference for Mn2+ over Mg2+. PPK2 shows no sequence similarity to PPK1 and belongs to a different superfamily. Pssm-ID: 197265 Cd Length: 163 Bit Score: 237.36 E-value: 1.19e-74
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| PLDc_PPK1_C1_unchar | cd09166 | Catalytic C-terminal domain, first repeat, of uncharacterized prokaryotic polyphosphate ... |
333-489 | 2.07e-66 | ||||||||||
Catalytic C-terminal domain, first repeat, of uncharacterized prokaryotic polyphosphate kinases; Catalytic C-terminal domain, first repeat (C1 domain), of a group of uncharacterized prokaryotic polyphosphate kinases (Poly P kinase 1 or PPK1, EC 2.7.4.1). Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. Pssm-ID: 197263 Cd Length: 162 Bit Score: 215.71 E-value: 2.07e-66
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| PLDc_PPK1_C2_unchar | cd09169 | Catalytic C-terminal domain, second repeat, of uncharacterized prokaryotic polyphosphate ... |
501-657 | 3.00e-59 | ||||||||||
Catalytic C-terminal domain, second repeat, of uncharacterized prokaryotic polyphosphate kinases; Catalytic C-terminal domain, second repeat (C2 domain), of a group of uncharacterized prokaryotic polyphosphate kinases (Poly P kinase 1 or PPK1, EC 2.7.4.1). Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. Pssm-ID: 197266 Cd Length: 162 Bit Score: 196.67 E-value: 3.00e-59
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| PP_kinase | pfam02503 | Polyphosphate kinase middle domain; Polyphosphate kinase (Ppk) catalyzes the formation of ... |
120-321 | 8.39e-42 | ||||||||||
Polyphosphate kinase middle domain; Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. Pssm-ID: 460574 [Multi-domain] Cd Length: 199 Bit Score: 150.67 E-value: 8.39e-42
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| PP_kinase_N | pfam13089 | Polyphosphate kinase N-terminal domain; Polyphosphate kinase (Ppk) catalyzes the formation of ... |
7-109 | 5.54e-35 | ||||||||||
Polyphosphate kinase N-terminal domain; Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. Pssm-ID: 463782 [Multi-domain] Cd Length: 106 Bit Score: 127.90 E-value: 5.54e-35
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| PLDc_unchar1_2 | cd09128 | Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ... |
351-488 | 5.89e-09 | ||||||||||
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. Pssm-ID: 197226 [Multi-domain] Cd Length: 142 Bit Score: 54.97 E-value: 5.89e-09
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| PLDc_SF | cd00138 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
351-475 | 9.80e-09 | ||||||||||
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. Pssm-ID: 197200 [Multi-domain] Cd Length: 119 Bit Score: 53.67 E-value: 9.80e-09
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| PLDc_unchar1_1 | cd09127 | Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ... |
345-489 | 8.20e-08 | ||||||||||
Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. Pssm-ID: 197225 [Multi-domain] Cd Length: 141 Bit Score: 51.88 E-value: 8.20e-08
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| Cls | COG1502 | Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ... |
379-523 | 2.38e-07 | ||||||||||
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis Pssm-ID: 441111 [Multi-domain] Cd Length: 367 Bit Score: 53.41 E-value: 2.38e-07
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| PLDc_2 | pfam13091 | PLD-like domain; |
369-489 | 8.65e-06 | ||||||||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 45.75 E-value: 8.65e-06
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| Cls | COG1502 | Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ... |
342-676 | 1.38e-05 | ||||||||||
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis Pssm-ID: 441111 [Multi-domain] Cd Length: 367 Bit Score: 48.01 E-value: 1.38e-05
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| PLDc_CLS_unchar1_2 | cd09162 | Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ... |
379-460 | 1.60e-04 | ||||||||||
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. Pssm-ID: 197259 [Multi-domain] Cd Length: 172 Bit Score: 43.02 E-value: 1.60e-04
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| PLDc_SF | cd00138 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
516-628 | 3.25e-04 | ||||||||||
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. Pssm-ID: 197200 [Multi-domain] Cd Length: 119 Bit Score: 40.96 E-value: 3.25e-04
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| PLDc_unchar3 | cd09131 | Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ... |
344-462 | 3.63e-04 | ||||||||||
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Pssm-ID: 197229 [Multi-domain] Cd Length: 143 Bit Score: 41.17 E-value: 3.63e-04
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| PLDc_CLS_2 | cd09112 | catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ... |
379-461 | 7.44e-03 | ||||||||||
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD corresponds to the catalytic domain repeat 2 of bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-) and a few homologs found in eukaryotes and archea. Bacterial CL synthases catalyze reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of conserved HKD motifs (H-X-K-X(4)-D, X represents any amino acid residue) that are the characteristic of the phospholipase D (PLD) superfamily. Two HKD motifs from two domains together form a single active site involving in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity in PLD superfamily. Like other PLD enzymes, bacterial CL synthase utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid stabilizing the leaving group. Pssm-ID: 197211 [Multi-domain] Cd Length: 174 Bit Score: 37.84 E-value: 7.44e-03
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