pcd1 (SPAC1556.04c; UniProt Q09190) encodes a putative zinc cytidine deaminase (EC 3.5.4.5), the ortholog of S. cerevisiae CDD1. It deaminates cytidine and deoxycytidine to uridine and deoxyuridine, routing pyrimidine nucleosides into uridine salvage. Function is assigned by orthology; it is cytosolic in a genome-wide screen.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004126 cytidine deaminase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference from characterised cytidine deaminases (S. cerevisiae CDD1); sound. Reason: UniProt annotates the cytidine deaminase reactions and a by-similarity (ECO:0000250) scavenging function, and the protein carries the tetrameric cytidine deaminase signature (TIGR01354) with by-similarity zinc-binding and active-site residues. No S. pombe-specific assay exists; the experimental basis is the characterised orthologs (e.g. S. cerevisiae CDD1). Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); file:SCHPO/pcd1/pcd1-uniprot.txt NCBIfam; TIGR01354; cyt_deam_tetra; 1. |
| GO:0004126 cytidine deaminase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC/ARBA mapping; consistent. Reason: Family membership and the annotated reaction support the mapping; no S. pombe-specific assay exists. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase family. file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); |
| GO:0005634 nucleus | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | KEEP AS NON CORE | Summary: ORFeome YFP screen recorded nuclear signal for pcd1. Soluble metabolic enzymes often show diffuse nucleocytoplasmic signal in this screen; no nuclear role is known. Reason: Experimental HDA kept, but not part of the core function. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA mapping; consistent with the screen. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005829 cytosol | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: ORFeome YFP screen placed pcd1 in the cytosol, consistent with a soluble metabolic enzyme. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of location; agrees with the localisation screen. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0006216 cytidine catabolic process | ISO GO_REF:0000024 | ACCEPT | Summary: Transfer from S. cerevisiae CDD1: cytidine deamination to uridine. Reason: UniProt's by-similarity function (ECO:0000250) and the cytidine-to-uridine reaction support cytidine catabolism; the ISO source is S. cerevisiae CDD1. No S. pombe-specific evidence. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); |
| GO:0006217 deoxycytidine catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference: deoxycytidine deamination. Reason: UniProt annotates the 2'-deoxycytidine deamination reaction and a by-similarity scavenging function covering 2'-deoxycytidine; no S. pombe-specific evidence. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=2'-deoxycytidine + H2O + H(+) = 2'-deoxyuridine + NH4(+); file:SCHPO/pcd1/pcd1-uniprot.txt This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Catalytic zinc cofactor of the cytidine deaminase active site; true but subsidiary to the deaminase activity. Reason: By similarity (ECO:0000250) to characterised cytidine deaminases, UniProt records a Zn(2+) cofactor and three catalytic zinc-binding residues (57, 89, 92) within the CMP/dCMP-type deaminase domain (PROSITE PS51747); no S. pombe-specific metal assay exists. Zinc binding is a cofactor property, kept as non-core. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250}; file:SCHPO/pcd1/pcd1-uniprot.txt PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | MODIFY | Summary: Generic InterPro-derived parent of the specific activity, which is already annotated. Reason: Hydrolase activity is correct but general; the specific hydrolytic deamination (EC 3.5.4.5, cytidine deaminase activity) is annotated by UniProt and rests on family membership (cytidine and deoxycytidylate deaminase family, TIGR01354) and similarity to characterised orthologs such as S. cerevisiae CDD1, not on an S. pombe assay. The gene already carries GO:0004126. Proposed replacements: cytidine deaminase activity Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); file:SCHPO/pcd1/pcd1-uniprot.txt SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase family. |
| GO:0042802 identical protein binding | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA mapping of identical protein binding, reflecting the homotetrameric quaternary structure of this cytidine deaminase subfamily; structural property. Reason: Rests on family membership only. pcd1 matches the tetrameric cytidine deaminase signatures (InterPro IPR006262, NCBIfam TIGR01354 cyt_deam_tetra), whose characterised members are homotetramers; no S. pombe oligomerisation data exist. Kept as non-core. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt InterPro; IPR006262; Cyt_deam_tetra. file:SCHPO/pcd1/pcd1-uniprot.txt NCBIfam; TIGR01354; cyt_deam_tetra; 1. |
| GO:0046109 uridine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference: cytidine deamination yields uridine. Reason: Deamination of cytidine yields uridine (annotated reaction), and UniProt's by-similarity function places the enzyme in nucleoside scavenging for UMP synthesis; no S. pombe-specific evidence. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); file:SCHPO/pcd1/pcd1-uniprot.txt This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. |
| GO:0055086 nucleobase-containing small molecule metabolic process | IEA GO_REF:0000117 | TOO GENERAL | Summary: True but uninformative ARBA parent; entailed by more specific nucleoside process terms. Reason: Entailed by cytidine and deoxycytidine catabolism (GO:0006216, GO:0006217) and uridine biosynthesis (GO:0046109), asserted elsewhere in this review. Those rest on the by-similarity (ECO:0000250) scavenging function and the annotated cytidine deamination reaction, i.e. similarity to characterised orthologs such as S. cerevisiae CDD1; no S. pombe-specific evidence. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); |
| GO:0072527 pyrimidine-containing compound metabolic process | IEA GO_REF:0000117 | TOO GENERAL | Summary: True but uninformative ARBA parent; entailed by more specific nucleoside process terms. Reason: Entailed by the pyrimidine nucleoside processes asserted elsewhere in this review (GO:0006216 cytidine catabolic process, GO:0006217, GO:0046109). Those rest on the by-similarity (ECO:0000250) scavenging function and the annotated cytidine deamination reaction, i.e. similarity to characterised orthologs such as S. cerevisiae CDD1; no S. pombe-specific evidence. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); |
| GO:1901135 carbohydrate derivative metabolic process | IEA GO_REF:0000117 | TOO GENERAL | Summary: True but uninformative ARBA parent; entailed by more specific nucleoside process terms. Reason: Entailed by the nucleoside (carbohydrate-derivative) processes asserted elsewhere in this review (GO:0006216 cytidine catabolic process, GO:0006217, GO:0046109). Those rest on the by-similarity (ECO:0000250) scavenging function and the annotated cytidine deamination reaction, i.e. similarity to characterised orthologs such as S. cerevisiae CDD1; no S. pombe-specific evidence. Supporting Evidence: file:SCHPO/pcd1/pcd1-uniprot.txt This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. file:SCHPO/pcd1/pcd1-uniprot.txt Reaction=cytidine + H2O + H(+) = uridine + NH4(+); |
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