pgaudet
commented
4 years ago Thanks for pointing this out @sjm41 I removed the MF for the alpha subunit genes, but kept the BP protein processing involved in protein targeting to mitochondrion.
Is that OK ?
Thanks, Pascale
sjm41
PTN000220169 adds "endopeptidase activity(CONTRIBUTES_TO)" to members of the METALLOPROTEASE (PTHR11851) family. PTHR11851 comprises both subunits from two homologous complexes - using humans as the example, those subunits are:
HUMAN|HGNC=18667|UniProtKB=Q10713 Mitochondrial-processing peptidase subunit alpha MITOCHONDRIAL-PROCESSING PEPTIDASE SUBUNIT ALPHA (PTHR11851:SF192)
HUMAN|HGNC=9119|UniProtKB=O75439 Mitochondrial-processing peptidase subunit beta MITOCHONDRIAL-PROCESSING PEPTIDASE SUBUNIT BETA (PTHR11851:SF103)
HUMAN|HGNC=12585|UniProtKB=P31930 Cytochrome b-c1 complex subunit 1, mitochondrial CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL (PTHR11851:SF116)
HUMAN|HGNC=12586|UniProtKB=P22695 Cytochrome b-c1 complex subunit 2, mitochondrial CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL (PTHR11851:SF216)
The source annotation for the ""endopeptidase activity" term comes from two C. elegans proteins:
Q95XN2 (mppa-1) contributes_to metalloendopeptidase activity IDA PMID:16788047
Q23295 (mppb-1) contributes_to metalloendopeptidase activity IDA PMID:16788047
Those annotations do represent the data from that 2006 paper, which says "Although neither the ZC410.2 (=mppb-1) nor the Y71G12B.24 (= mppa-1) protein showed any proteolytic activity independently (Fig. 5, A and B), a mixture of the two proteins was found to cleave a substrate peptide...Therefore, the metallopeptidase activity of MPP is suggested to depend on the association of the ZC410.2 and Y71G12B.24 proteins."
However, the wider/deeper understanding (as stated in the introduction to that worm paper) is that: i) peptidase activity of the MITOCHONDRIAL-PROCESSING PEPTIDASE complex is restricted to the beta subunit (= human O75439/PMPCB) ii) peptidase activity of the CYTOCHROME B-C1 COMPLEX is either restricted to the homologous subunit (= human P31930/UQCRC1) or is absent from this complex. (see PMID:12191769 for a review, and the intro to PMID:16788047; also see UniProt webpages for Q10713 & O75439, and P31930 & P22695)
So...I think the propagation of "endopeptidase activity(CONTRIBUTES_TO)" should either be blocked on this node, or else the PANTHER family needs splitting out and GO terms assigned appropriately.
@hattrill