3MHS
Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000124 | cellular_component | SAGA complex |
| A | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| A | 0006508 | biological_process | proteolysis |
| A | 0008233 | molecular_function | peptidase activity |
| A | 0008234 | molecular_function | cysteine-type peptidase activity |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0008380 | biological_process | RNA splicing |
| A | 0016579 | biological_process | protein deubiquitination |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0060090 | molecular_function | molecular adaptor activity |
| A | 0071819 | cellular_component | DUBm complex |
| B | 0000124 | cellular_component | SAGA complex |
| B | 0000932 | cellular_component | P-body |
| B | 0000973 | biological_process | post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery |
| B | 0003682 | molecular_function | chromatin binding |
| B | 0003713 | molecular_function | transcription coactivator activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005643 | cellular_component | nuclear pore |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| B | 0006368 | biological_process | transcription elongation by RNA polymerase II |
| B | 0006406 | biological_process | mRNA export from nucleus |
| B | 0008047 | molecular_function | enzyme activator activity |
| B | 0015031 | biological_process | protein transport |
| B | 0016973 | biological_process | poly(A)+ mRNA export from nucleus |
| B | 0032880 | biological_process | regulation of protein localization |
| B | 0043229 | cellular_component | intracellular organelle |
| B | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| B | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| B | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| B | 0051028 | biological_process | mRNA transport |
| B | 0070390 | cellular_component | transcription export complex 2 |
| B | 0071028 | biological_process | nuclear mRNA surveillance |
| B | 0071819 | cellular_component | DUBm complex |
| C | 0000124 | cellular_component | SAGA complex |
| C | 0003713 | molecular_function | transcription coactivator activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0006325 | biological_process | chromatin organization |
| C | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| C | 0008047 | molecular_function | enzyme activator activity |
| C | 0008270 | molecular_function | zinc ion binding |
| C | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| C | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0070461 | cellular_component | SAGA-type complex |
| C | 0071819 | cellular_component | DUBm complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1295 |
| Chain | Residue |
| A | GLN236 |
| A | GLU240 |
| D | ARG74 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1487 |
| Chain | Residue |
| A | HIS367 |
| A | LEU369 |
| A | GLY371 |
| A | HOH562 |
| D | GLY35 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 472 |
| Chain | Residue |
| A | HIS6 |
| A | CYS96 |
| A | CYS99 |
| A | CYS4 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 473 |
| Chain | Residue |
| A | CYS46 |
| A | CYS49 |
| A | CYS68 |
| A | HIS73 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 474 |
| Chain | Residue |
| A | CYS60 |
| A | CYS63 |
| A | HIS77 |
| A | HIS83 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 475 |
| Chain | Residue |
| A | HIS170 |
| A | CYS174 |
| A | CYS182 |
| A | CYS185 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 476 |
| Chain | Residue |
| A | HIS250 |
| A | CYS271 |
| A | CYS273 |
| A | HIS276 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 100 |
| Chain | Residue |
| C | CYS73 |
| C | CYS76 |
| C | HIS88 |
| C | CYS92 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN E 97 |
| Chain | Residue |
| E | CYS78 |
| E | CYS81 |
| E | HIS93 |
| E | GLU95 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 477 |
| Chain | Residue |
| A | CYS289 |
| A | CYS292 |
| A | CYS336 |
| A | CYS339 |
Functional Information from PROSITE/UniProt
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| D | LYS27-ASP52 |
| site_id | PS00972 |
| Number of Residues | 16 |
| Details | USP_1 Ubiquitin specific protease (USP) domain signature 1. GLinmGStCFMSSiLQ |
| Chain | Residue | Details |
| A | GLY138-GLN153 |
| site_id | PS00973 |
| Number of Residues | 18 |
| Details | USP_2 Ubiquitin specific protease (USP) domain signature 2. YeLiGIvsHkGtvne..GHY |
| Chain | Residue | Details |
| A | TYR411-TYR428 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | SITE: Interacts with activating enzyme |
| Chain | Residue | Details |
| D | ARG54 | |
| D | ARG72 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | SITE: Essential for function |
| Chain | Residue | Details |
| D | HIS68 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 |
| Chain | Residue | Details |
| D | SER65 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 |
| Chain | Residue | Details |
| D | THR66 | |
| A | CYS49 | |
| A | CYS60 | |
| A | CYS63 | |
| A | CYS68 | |
| A | HIS73 | |
| A | HIS77 | |
| A | HIS83 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742 |
| Chain | Residue | Details |
| D | GLZ76 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 |
| Chain | Residue | Details |
| D | LYS6 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) |
| Chain | Residue | Details |
| D | GLZ76 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 |
| Chain | Residue | Details |
| D | LYS11 | |
| D | LYS48 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 |
| Chain | Residue | Details |
| D | LYS27 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 |
| Chain | Residue | Details |
| D | LYS29 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 |
| Chain | Residue | Details |
| D | LYS33 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 |
| Chain | Residue | Details |
| D | LYS63 |
