purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA); ...
20-281
1.98e-139
purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA); Human PNP catalyzes the reversible phosphorolysis of the purine nucleosides and deoxynucleosides inosine, guanosine, deoxyinosine, and deoxyguanosine. Patients with PNP deficiency typically present with severe immunodeficiency, neurological dysfunction, and autoimmunity. Escherichia coli PNPII, product of the xapA/pndA gene, catalyzes the phosphorolysis of xanthosine, inosine and guanosine with equal efficiency and has been referred to as xanthosine phosphorylase and inosine-guanosine phosphorylase. E. coli PNPII is also capable of converting nicotinamide to nicotinamide riboside, and may be involved in the NAD+ salvage pathway. It is one of two purine nucleoside phosphorylases found in E. coli, which also contains PNPI, which displays a different substrate specificity and belongs to a different subgroup of the nucleoside phosphorylase-I (NP-I) family than PNPII. NP-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family.
Pssm-ID: 350160 Cd Length: 265 Bit Score: 393.30 E-value: 1.98e-139
inosine/guanosine/xanthosine phosphorylase family; This model is a subset of the subfamily ...
34-282
1.56e-126
inosine/guanosine/xanthosine phosphorylase family; This model is a subset of the subfamily represented by pfam00896 (phosphorylase family 2). This model excludes the methylthioadenosine phosphorylases (MTAP, TIGR01684) which are believed toplay a specific role in the recycling of methionine from methylthioadenosine. In this subfamily is found three clades of purine phosphorylases based on a neighbor-joining tree using the MTAP family as an outgroup. The highest-branching clade (TIGR01698) consists of a group of sequences from both gram positive and gram negative bacteria which have been annotated as purine nucleotide phosphorylases but have not been further characterized as to substrate specificity. Of the two remaining clades, one is xanthosine phosphorylase (XAPA, TIGR01699), is limited to certain gamma proteobacteria and constitutes a special purine phosphorylase found in a specialized operon for xanthosine catabolism. The enzyme also acts on the same purines (inosine and guanosine) as the other characterized members of this subfamily, but is only induced when xanthosine must be degraded. The remaining and largest clade consists of purine nucleotide phosphorylases (PNPH, TIGR01700) from metazoa and bacteria which act primarily on guanosine and inosine (and do not act on adenosine). Sequences from Clostridium (GP:15025051) and Thermotoga (OMNI:TM1596) fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Pssm-ID: 130758 Cd Length: 248 Bit Score: 360.13 E-value: 1.56e-126
Purine nucleoside phosphorylase [Nucleotide transport and metabolism]; Purine nucleoside ...
36-283
4.02e-101
Purine nucleoside phosphorylase [Nucleotide transport and metabolism]; Purine nucleoside phosphorylase is part of the Pathway/BioSystem: Purine salvage
Pssm-ID: 439776 Cd Length: 241 Bit Score: 295.43 E-value: 4.02e-101
Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase ...
34-282
3.49e-45
Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Pssm-ID: 426013 Cd Length: 233 Bit Score: 152.50 E-value: 3.49e-45
purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA); ...
20-281
1.98e-139
purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA); Human PNP catalyzes the reversible phosphorolysis of the purine nucleosides and deoxynucleosides inosine, guanosine, deoxyinosine, and deoxyguanosine. Patients with PNP deficiency typically present with severe immunodeficiency, neurological dysfunction, and autoimmunity. Escherichia coli PNPII, product of the xapA/pndA gene, catalyzes the phosphorolysis of xanthosine, inosine and guanosine with equal efficiency and has been referred to as xanthosine phosphorylase and inosine-guanosine phosphorylase. E. coli PNPII is also capable of converting nicotinamide to nicotinamide riboside, and may be involved in the NAD+ salvage pathway. It is one of two purine nucleoside phosphorylases found in E. coli, which also contains PNPI, which displays a different substrate specificity and belongs to a different subgroup of the nucleoside phosphorylase-I (NP-I) family than PNPII. NP-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family.
Pssm-ID: 350160 Cd Length: 265 Bit Score: 393.30 E-value: 1.98e-139
inosine/guanosine/xanthosine phosphorylase family; This model is a subset of the subfamily ...
34-282
1.56e-126
inosine/guanosine/xanthosine phosphorylase family; This model is a subset of the subfamily represented by pfam00896 (phosphorylase family 2). This model excludes the methylthioadenosine phosphorylases (MTAP, TIGR01684) which are believed toplay a specific role in the recycling of methionine from methylthioadenosine. In this subfamily is found three clades of purine phosphorylases based on a neighbor-joining tree using the MTAP family as an outgroup. The highest-branching clade (TIGR01698) consists of a group of sequences from both gram positive and gram negative bacteria which have been annotated as purine nucleotide phosphorylases but have not been further characterized as to substrate specificity. Of the two remaining clades, one is xanthosine phosphorylase (XAPA, TIGR01699), is limited to certain gamma proteobacteria and constitutes a special purine phosphorylase found in a specialized operon for xanthosine catabolism. The enzyme also acts on the same purines (inosine and guanosine) as the other characterized members of this subfamily, but is only induced when xanthosine must be degraded. The remaining and largest clade consists of purine nucleotide phosphorylases (PNPH, TIGR01700) from metazoa and bacteria which act primarily on guanosine and inosine (and do not act on adenosine). Sequences from Clostridium (GP:15025051) and Thermotoga (OMNI:TM1596) fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Pssm-ID: 130758 Cd Length: 248 Bit Score: 360.13 E-value: 1.56e-126
xanthosine phosphorylase; This model represents a small clade of purine nucleotide ...
36-282
6.31e-117
xanthosine phosphorylase; This model represents a small clade of purine nucleotide phosphorylases found in certain gamma proteobacteria. The gene is part of an operon for the degradation of xanthosine and is induced by xanthosine. The enzyme is also capable of acting on inosine and guanosine (but not adenosine) in a manner similar to those other phosphorylases to which it is closely related (TIGR01698, TIGR01700).
Pssm-ID: 130760 Cd Length: 248 Bit Score: 335.87 E-value: 6.31e-117
Purine nucleoside phosphorylase [Nucleotide transport and metabolism]; Purine nucleoside ...
36-283
4.02e-101
Purine nucleoside phosphorylase [Nucleotide transport and metabolism]; Purine nucleoside phosphorylase is part of the Pathway/BioSystem: Purine salvage
Pssm-ID: 439776 Cd Length: 241 Bit Score: 295.43 E-value: 4.02e-101
purine nucleoside phosphorylase I, inosine and guanosine-specific; This model represents a ...
34-281
1.53e-96
purine nucleoside phosphorylase I, inosine and guanosine-specific; This model represents a family of bacterial and metazoan purine phosphorylases acting primarily on inosine and guanosine and not acting on adenosine. PNP-I refers to the nomenclature from Bacillus stearothermophilus where PHP-II refers to the nucleotidase acting on adenosine as the primary substrate.The bacterial enzymes (PUNA) are typified by the Bacilus PupG protein, which is involved in the metabolism of nucleosides as a carbon source.Several metazoan enzymes (PNPH) are well characterized including the human and bovine enzymes which have been crystallized. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides]
Pssm-ID: 273764 Cd Length: 249 Bit Score: 284.36 E-value: 1.53e-96
purine nucleotide phosphorylase; This clade of purine nucleotide phosphorylases has not been ...
36-282
2.62e-79
purine nucleotide phosphorylase; This clade of purine nucleotide phosphorylases has not been experimentally characterized but is assigned based on strong sequence homology. Closely related clades act on inosine and guanosine (PNPH, TIGR01700), and xanthosine, inosine and guanosine (XAPA, TIGR01699) neither of these will act on adenosine. A more distantly related clade (MTAP, TIGR01694) acts on methylthioadenosine.
Pssm-ID: 130759 Cd Length: 237 Bit Score: 240.11 E-value: 2.62e-79
Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase ...
34-282
3.49e-45
Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Pssm-ID: 426013 Cd Length: 233 Bit Score: 152.50 E-value: 3.49e-45
5'-deoxy-5'-methylthioadenosine phosphorylases (MTAP) similar to Sulfolobus solfataricus ...
36-281
8.76e-38
5'-deoxy-5'-methylthioadenosine phosphorylases (MTAP) similar to Sulfolobus solfataricus MTAPII and Pseudomonas aeruginosa PAO1 5'-methylthioinosine phosphorylase (MTIP); MTAP catalyzes the reversible phosphorolysis of 5'-deoxy-5'-methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1-phosphate. This subfamily includes human MTAP which is highly specific for MTA, and Sulfolobus solfataricus MTAPII which accepts adenosine in addition to MTA. Two MTAPs have been isolated from S. solfataricus: SsMTAP1 and SsMTAPII, SsMTAP1 belongs to a different subfamily of the nucleoside phosphorylase-I (NP-I) family. This group also includes Pseudomonas aeruginosa PAO1 MTI phosphorylase (MTIP) which uses 5'-methylthioinosine (MTI) as a preferred substrate, and does not use MTA. NP-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family.
Pssm-ID: 350161 Cd Length: 238 Bit Score: 133.31 E-value: 8.76e-38
5'-deoxy-5'-methylthioadenosine phosphorylase; This model represents the methylthioadenosine ...
36-282
8.87e-25
5'-deoxy-5'-methylthioadenosine phosphorylase; This model represents the methylthioadenosine phosphorylase found in metazoa, cyanobacteria and a limited number of archaea such as Sulfolobus, Aeropyrum, Pyrobaculum, Pyrococcus, and Thermoplasma. This enzyme is responsible for the first step in the methionine salvage pathway after the transfer of the amino acid moiety from S-adenosylmethionine. The enzyme from human is well-characterized including a crystal structure. A misleading characterization is found for a Sulfolobus solfataricus enzyme, which is called a MTAP. In fact, as uncovered by the genome sequence of S. solfataricus, there are at least two nucleotide phosphorylases and the one found in the MTAP clade is not the one annotated as such. The sequence in this clade has not been isolated but is likely to be the authentic SsMTAP as it displays all of the conserved active site residues found in the human enzyme. This explains the finding that the characterized enzyme has greater efficiency towards the purines inosine, guanosine and adenosine over MTA. In fact, this mis-naming of this enzyme has been carried forward to several publications including a crystal stucture. In between the trusted and noise cutoffs are: 1) several archaeal sequences which appear to contain several residues characteristic of phosphorylases which act on guanosine or inosine (according to the crystal structure of MTAP and alignments). In any case, these residues are not conserved. 2) sequences from Mycobacterium tuberculosis and Streptomyces coelicolor which have better, although not perfect retention of the active site residues, but considering the general observation that bacteria utilize the MTA/SAH nucleotidase enzyme and a kinase to do this reaction, these have been excluded pending stronger evidence of their function, and 3) a sequence from Drosophila which appears to be a recent divergence (long branch in neighbor-joining trees) and lacks some of the conserved active site residues. [Central intermediary metabolism, Other, Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides]
Pssm-ID: 273762 Cd Length: 241 Bit Score: 99.33 E-value: 8.87e-25
nucleoside phosphorylase-I family; The nucleoside phosphorylase-I family members accept a ...
71-271
7.48e-21
nucleoside phosphorylase-I family; The nucleoside phosphorylase-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases such as purine nucleoside phosphorylase (PNP, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases such as AMP nucleosidase (AMN, EC 3.2.2.4) and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). Members of this family display different physiologically relevant quaternary structures: hexameric (trimer-of-dimers arrangement of Shewanella oneidensis MR-1 UP); homotrimeric (human PNP and Escherichia coli PNPII or XapA); hexameric (with some evidence for co-existence of a trimeric form) such as E. coli PNPI (DeoD); or homodimeric such as human and Trypanosoma brucei UP. The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family.
Pssm-ID: 350156 Cd Length: 216 Bit Score: 88.12 E-value: 7.48e-21
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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