1WYW
Crystal Structure of SUMO1-conjugated thymine DNA glycosylase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000700 | molecular_function | mismatch base pair DNA N-glycosylase activity |
| A | 0006285 | biological_process | base-excision repair, AP site formation |
| B | 0001741 | cellular_component | XY body |
| B | 0003723 | molecular_function | RNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005643 | cellular_component | nuclear pore |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006281 | biological_process | DNA repair |
| B | 0006355 | biological_process | regulation of DNA-templated transcription |
| B | 0008076 | cellular_component | voltage-gated potassium channel complex |
| B | 0008134 | molecular_function | transcription factor binding |
| B | 0010621 | biological_process | negative regulation of transcription by transcription factor localization |
| B | 0015459 | molecular_function | potassium channel regulator activity |
| B | 0016604 | cellular_component | nuclear body |
| B | 0016605 | cellular_component | PML body |
| B | 0016607 | cellular_component | nuclear speck |
| B | 0016925 | biological_process | protein sumoylation |
| B | 0019899 | molecular_function | enzyme binding |
| B | 0030578 | biological_process | PML body organization |
| B | 0031334 | biological_process | positive regulation of protein-containing complex assembly |
| B | 0031386 | molecular_function | protein tag activity |
| B | 0031625 | molecular_function | ubiquitin protein ligase binding |
| B | 0031647 | biological_process | regulation of protein stability |
| B | 0031965 | cellular_component | nuclear membrane |
| B | 0032436 | biological_process | positive regulation of proteasomal ubiquitin-dependent protein catabolic process |
| B | 0032880 | biological_process | regulation of protein localization |
| B | 0034605 | biological_process | cellular response to heat |
| B | 0042308 | biological_process | negative regulation of protein import into nucleus |
| B | 0043392 | biological_process | negative regulation of DNA binding |
| B | 0043433 | biological_process | negative regulation of DNA-binding transcription factor activity |
| B | 0044388 | molecular_function | small protein activating enzyme binding |
| B | 0044389 | molecular_function | ubiquitin-like protein ligase binding |
| B | 0045759 | biological_process | negative regulation of action potential |
| B | 0045892 | biological_process | negative regulation of DNA-templated transcription |
| B | 0050821 | biological_process | protein stabilization |
| B | 0060021 | biological_process | roof of mouth development |
| B | 0071276 | biological_process | cellular response to cadmium ion |
| B | 0086004 | biological_process | regulation of cardiac muscle cell contraction |
| B | 0090204 | biological_process | protein localization to nuclear pore |
| B | 0097165 | cellular_component | nuclear stress granule |
| B | 0098978 | cellular_component | glutamatergic synapse |
| B | 0099523 | cellular_component | presynaptic cytosol |
| B | 0099524 | cellular_component | postsynaptic cytosol |
| B | 1901017 | biological_process | negative regulation of potassium ion transmembrane transporter activity |
| B | 1902260 | biological_process | negative regulation of delayed rectifier potassium channel activity |
| B | 1903169 | biological_process | regulation of calcium ion transmembrane transport |
| B | 1990381 | molecular_function | ubiquitin-specific protease binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL A 340 |
| Chain | Residue |
| A | LYS232 |
| A | SER271 |
| A | HOH450 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL A 341 |
| Chain | Residue |
| A | GLY154 |
| A | HIS175 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL A 342 |
| Chain | Residue |
| A | LEU120 |
| A | LEU254 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA B 204 |
| Chain | Residue |
| B | LYS48 |
| B | ASP73 |
| A | LYS246 |
| A | HOH477 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MG A 343 |
| Chain | Residue |
| A | GLN283 |
| A | ASP284 |
| A | LYS285 |
| A | VAL286 |
| A | HIS287 |
| A | TYR313 |
| A | HOH348 |
| B | ARG54 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 206 |
| Chain | Residue |
| B | HIS43 |
| B | HOH209 |
| B | HOH212 |
| B | HOH240 |
| B | HOH241 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 207 |
| Chain | Residue |
| B | HOH210 |
| B | HOH211 |
| B | HOH225 |
| B | HOH227 |
| B | HOH233 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG B 208 |
| Chain | Residue |
| B | THR76 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 344 |
| Chain | Residue |
| A | ILE136 |
| A | GLY138 |
| A | TYR152 |
| A | THR190 |
| A | ASN191 |
| A | HOH349 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | SITE: Interaction with PIAS2 |
| Chain | Residue | Details |
| B | PHE36 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:18707152, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER2 | |
| A | LYS330 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| B | SER9 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER32 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS7 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) => ECO:0000269|PubMed:27068747 |
| Chain | Residue | Details |
| B | GLY97 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS16 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS17 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS23 | |
| B | LYS39 | |
| B | LYS45 | |
| B | LYS46 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1) |
| Chain | Residue | Details |
| B | LYS25 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS37 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 2 |
| Details | M-CSA 834 |
| Chain | Residue | Details |
| A | ASN140 | electrostatic interaction |
| A | HIS151 | proton acceptor, proton donor |
