Table 2.
Analysis of cleavage sites of known granzyme B substrates with GraBCas
| Granzyme B substrate | Acc_number | Known cleavage site | Score by GraBCas | P6–P2′ of cleavage site |
|---|---|---|---|---|
| AARS: alanyl-tRNA synthetase | NP_001596 | VADP (632) | 7,65 | SLVAPDRL |
| ADPRT: ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) | NP_001609 | VDPD (536) | 9,9 | AAVDPDSG |
| BID: BH3 interacting domain death agonist | NP_001187 | IEAD (75) | 57,6 | GRIEADSE |
| CASP3: caspase 3, apoptosis-related cysteine protease | NP_004337 | IETD (175) | 54,4 | CGIETDSG |
| CASP7: caspase 7, apoptosis-related cysteine protease | NP_001218 | IQAD (198) | 4,6656 | DGIQADSG |
| CENPB: centromere protein B, 80 kDa | NP_001801 | VDSD (457) | 7,4448 | GDVDSDEE |
| CHD4: chromodomain helicase DNA binding protein 4 | NP_001264 | VDPD (1312) | 9,9 | ESVDPDYW |
| DFFA: DNA fragmentation factor, 45 kDa, alpha polypeptide | NP_004392 | DETD (117) | 0,0544 | MEVTGDAG |
| DFFA: DNA fragmentation factor, 45 kDa, alpha polypeptide | NP_004392 | VTGD (6) | 0,0432 | DVDETDSG |
| FBL: fibrillarin | NP_001427 | VGPD (184) | 23,85 | DIVGPDGL |
| FLNA: filamin A, alpha (actin binding protein 280) | NP_001447 | ? | 11,4048 | TEIDQDKY |
| G22P1: thyroid autoantigen 70 kDa (Ku antigen) | NP_001460 | ISSD (79) | 22,3344 | KIISSDRD |
| GRIA3: glutamate receptor, ionotrophic, AMPA 3 | NP_000819 | ISND (416) | 18,5328 | QQISNDSA |
| HARS: histidyl-tRNA synthetase | NP_002100 | LGPD (48) | 2,4804 | AQLGPDES |
| IARS: isoleucine-tRNA synthetase | NP_002152 | VTPD (983) | 2,7 | LDVTPDQS |
| L4 100K [Human adenovirus C] | AAQ19301 | IEQD (48) | 57,6 | VIIEQDPG |
| MKI67: antigen identified by monoclonal antibody Ki-67 | NP_002408 | VCTD (1481) | 0,0272 | TPVCTDKP |
| NUMA1: nuclear mitotic apparatus protein 1 | NP_006176 | VATD (1705) | 4,1616 | FQVATDAL |
| PMS1: PMS1 postmeiotic segregation increased 1 | NP_000525 | ISAD (496) | 17,1072 | SEISADEW |
| PMS2: PMS2 postmeiotic segregation increased 2 | NP_000526 | VEKD (493) | 0,05 | AEVEKDSG |
| PMSCL2: polymyositis/scleroderma autoantigen 2, 100 kDa | NP_002676 | VEQD (252) | 28,8 | QQVEQDMF |
| POLR1A: polymerase (RNA) I polypeptide A, 194 kDa | NP_056240 | ICPD (448) | 0,1 | SVICPDMY |
| POLR2A: polymerase (RNA) II (DNA directed) polypeptide A, 220 kDa | NP_000928 | ITPD (370) | 5,4 | TVITPDPN |
| PRKDC: protein kinase, DNA-activated, catalytic polypeptide | NP_008835 | VGPD (2698) | 23,85 | KSVGPDFG |
| SNRP70: small nuclear ribonucleoprotein 70 kDa polypeptide (RNP antigen) | NP_003080 | LGND (409) | 1,5477696 | EGLGNDSR |
| SRP72: signal recognition particle 72 kDa | NP_008878 | VTPD (573) | 2,7 | PKVTPDPE |
| SSB: Sjogren syndrome antigen B (autoantigen La) | NP_003133 | LEED (220) | 1,4976 | QKLEEDAE |
| TOP1: topoisomerase (DNA) I | NP_003277 | IEAD (15) | 57,6 | SQIEADFR |
| UBE4B: ubiquitination factor E4B (UFD2 homolog, yeast) | NP_006039 | VDVD (123) | 3,0096 | SQVDVDSG |
| UBTF: upstream binding transcription factor, RNA polymerase I | NP_055048 | VRPD (220) | 0,05 | LKVRPDAT |
The bold printed amino acids in the extended cleavage site indicate hits with a G residue at position P2′ detected by the high stringency filter. Numbers in brackets indicate cleavage site position in the amino acid sequence.