# HISTORY 23 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.12 # molecular_function 20110123: root_PTN000000113 has function zinc ion binding (GO:0008270) 20110123: root_PTN000000113 has function copper ion binding (GO:0005507) 20110123: root_PTN000000113 has function superoxide dismutase activity (GO:0004784) # cellular_component 20140505: cellular organisms_PTN000000114 is found in cytoplasm (GO:0005737) 20140505: Euteleostomi_PTN000796844 is found in extracellular space (GO:0005615) 20140505: Bacteria _PTN000000276 is found in periplasmic space (GO:0042597) # biological_process 20110123: root_PTN000000113 participates in removal of superoxide radicals (GO:0019430) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES Fast-pass curation of PTHR10003 (superoxide dismutase family): Description of phylogeny This family has a bacterial outgroup (represented by E. coli sodC) and two paralogous clades that span plants to humans. The AN3 clade is simple, contains no duplications, and seems to consist of copper chaperones for superoxide dismutase. The AN46 clade consists of copper-zinc superoxide dismutases and contains a duplication at the vertebrate common ancestor, AN53; the divergent AN54 clade contains extracellular Cu-Zn SOD's. MF -Propagate GO:0004784 "superoxide dismutase activity" to root, and add NOT 'superoxide dismutase activity (GO:0004784)' by IKR on Eukaryota_PTN000000116. The catalytic site of SOD is actually the metal ion cofactor, not part of the protein itself. (See http://en.wikipedia.org/wiki/Superoxide_dismutase). E. coli sodC and the eukaryotic SODs have 4 copper-binding histidines at E. coli positions 67, 69, 92, and 147, corresponding approximately to positions 320 (for 67 and 69), 348, and 470 in this alignment. (See UniProt and EcoCyc.) In the CCS clade, the first three histidines are present in rat, mouse, human, and fly (metazoa), and several of the other sites are also still histidines in dicty, yeast, and pombe, but none of them is annotated as a metal ion binding site. Copper binding in the CCS clade appears to be via 2 pairs of cysteine residues (22/25 and 244/246) in human, mouse, and rat (same numebring in all three), and nearby residues in dicty, yeast, and pombe. -Also propagate GO:0008270 "zinc ion binding" to AN0. In the absence of contradictory information, allow this to propagate to the CCS clade, but be prepared to change this decision. BP - Start with functions directly related to the MFs of these proteins. Set aside multicellular processes. - Propagate to root: GO:0019430 "removal of superoxide radicals" - No BP specific for CCS clade: it is not a copper transporter as many annotations suggest. It delivers copper to SOD, which is covered by MF, and is still part of the same overall BP annotated to root. CC - PG Removed all previous annotations (many were clade-specific with little evidence) - Propagated 'periplasmic space (GO:0042597)' in Bacteria _PTN000000276 since all have a signal sequence - TO DO: I would have liked to 'not' cytoplasm (GO:0005737) in cellular organisms_PTN000000114, but PAINT does not allow me. Pruned root_PTN000000215 : sequences deleted from uniProt. Submitted 2010-09-28, MSL Updated 2010-12-22, MSL Updated 2011-03-09, MSL Updated 2011-06-13, PDT Reviewed 2014-05-05 PG # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).