1Q2R
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0006400 | biological_process | tRNA modification |
| A | 0008033 | biological_process | tRNA processing |
| A | 0008479 | molecular_function | tRNA-guanosine(34) queuine transglycosylase activity |
| A | 0008616 | biological_process | queuosine biosynthetic process |
| A | 0016757 | molecular_function | glycosyltransferase activity |
| A | 0016763 | molecular_function | pentosyltransferase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0101030 | biological_process | tRNA-guanine transglycosylation |
| B | 0006400 | biological_process | tRNA modification |
| B | 0008033 | biological_process | tRNA processing |
| B | 0008479 | molecular_function | tRNA-guanosine(34) queuine transglycosylase activity |
| B | 0008616 | biological_process | queuosine biosynthetic process |
| B | 0016757 | molecular_function | glycosyltransferase activity |
| B | 0016763 | molecular_function | pentosyltransferase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0101030 | biological_process | tRNA-guanine transglycosylation |
| C | 0006400 | biological_process | tRNA modification |
| C | 0008033 | biological_process | tRNA processing |
| C | 0008479 | molecular_function | tRNA-guanosine(34) queuine transglycosylase activity |
| C | 0008616 | biological_process | queuosine biosynthetic process |
| C | 0016757 | molecular_function | glycosyltransferase activity |
| C | 0016763 | molecular_function | pentosyltransferase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0101030 | biological_process | tRNA-guanine transglycosylation |
| D | 0006400 | biological_process | tRNA modification |
| D | 0008033 | biological_process | tRNA processing |
| D | 0008479 | molecular_function | tRNA-guanosine(34) queuine transglycosylase activity |
| D | 0008616 | biological_process | queuosine biosynthetic process |
| D | 0016757 | molecular_function | glycosyltransferase activity |
| D | 0016763 | molecular_function | pentosyltransferase activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0101030 | biological_process | tRNA-guanine transglycosylation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 401 |
| Chain | Residue |
| A | CYS318 |
| A | CYS320 |
| A | CYS323 |
| A | HIS349 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE 9DG A 387 |
| Chain | Residue |
| A | ILE201 |
| A | GLN203 |
| A | GLY229 |
| A | GLY230 |
| A | MET260 |
| A | ASP102 |
| A | SER103 |
| A | TYR106 |
| A | ASP156 |
| A | CYS158 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 402 |
| Chain | Residue |
| B | CYS318 |
| B | CYS320 |
| B | CYS323 |
| B | HIS349 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 9DG B 387 |
| Chain | Residue |
| B | ASP102 |
| B | TYR106 |
| B | ASP156 |
| B | CYS158 |
| B | ILE201 |
| B | GLY230 |
| B | MET260 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 403 |
| Chain | Residue |
| C | CYS318 |
| C | CYS320 |
| C | CYS323 |
| C | HIS349 |
| site_id | AC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE 9DG C 387 |
| Chain | Residue |
| C | ASP102 |
| C | SER103 |
| C | GLY105 |
| C | TYR106 |
| C | ASP156 |
| C | CYS158 |
| C | ILE201 |
| C | GLN203 |
| C | GLY229 |
| C | GLY230 |
| C | MET260 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 404 |
| Chain | Residue |
| D | CYS318 |
| D | CYS320 |
| D | CYS323 |
| D | HIS349 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE 9DG D 387 |
| Chain | Residue |
| D | ASP102 |
| D | TYR106 |
| D | ASP156 |
| D | CYS158 |
| D | ILE201 |
| D | GLN203 |
| D | GLY229 |
| D | GLY230 |
| D | MET260 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255|HAMAP-Rule:MF_00168, ECO:0000305|PubMed:12949492 |
| Chain | Residue | Details |
| A | SER103 | |
| B | SER103 | |
| C | SER103 | |
| D | SER103 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000255|HAMAP-Rule:MF_00168, ECO:0000305|PubMed:12949492 |
| Chain | Residue | Details |
| A | CYS281 | |
| B | CYS281 | |
| C | CYS281 | |
| D | CYS281 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00168, ECO:0000269|PubMed:12949492 |
| Chain | Residue | Details |
| A | SER103 | |
| C | GLU157 | |
| C | GLY204 | |
| C | LEU231 | |
| D | SER103 | |
| D | GLU157 | |
| D | GLY204 | |
| D | LEU231 | |
| A | GLU157 | |
| A | GLY204 | |
| A | LEU231 | |
| B | SER103 | |
| B | GLU157 | |
| B | GLY204 | |
| B | LEU231 | |
| C | SER103 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00168, ECO:0000269|PubMed:10413112, ECO:0000269|PubMed:11178905, ECO:0000269|PubMed:11921407, ECO:0000269|PubMed:12646024, ECO:0000269|PubMed:12909636, ECO:0000269|PubMed:12949492, ECO:0000269|PubMed:14523925, ECO:0000269|PubMed:19627989, ECO:0000269|PubMed:8654383, ECO:0000269|PubMed:8961936 |
| Chain | Residue | Details |
| A | HIS319 | |
| C | ALA321 | |
| C | GLN324 | |
| C | ASN350 | |
| D | HIS319 | |
| D | ALA321 | |
| D | GLN324 | |
| D | ASN350 | |
| A | ALA321 | |
| A | GLN324 | |
| A | ASN350 | |
| B | HIS319 | |
| B | ALA321 | |
| B | GLN324 | |
| B | ASN350 | |
| C | HIS319 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1pud |
| Chain | Residue | Details |
| A | ASP102 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1pud |
| Chain | Residue | Details |
| B | ASP102 |
| site_id | CSA3 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1pud |
| Chain | Residue | Details |
| C | ASP102 |
| site_id | CSA4 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1pud |
| Chain | Residue | Details |
| D | ASP102 |
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 881 |
| Chain | Residue | Details |
| A | SER103 | proton shuttle (general acid/base) |
| A | CYS281 | covalent catalysis |
| A | HIS319 | metal ligand |
| A | ALA321 | metal ligand |
| A | GLN324 | metal ligand |
| A | ASN350 | metal ligand |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 881 |
| Chain | Residue | Details |
| B | SER103 | proton shuttle (general acid/base) |
| B | CYS281 | covalent catalysis |
| B | HIS319 | metal ligand |
| B | ALA321 | metal ligand |
| B | GLN324 | metal ligand |
| B | ASN350 | metal ligand |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 881 |
| Chain | Residue | Details |
| C | SER103 | proton shuttle (general acid/base) |
| C | CYS281 | covalent catalysis |
| C | HIS319 | metal ligand |
| C | ALA321 | metal ligand |
| C | GLN324 | metal ligand |
| C | ASN350 | metal ligand |
| site_id | MCSA4 |
| Number of Residues | 6 |
| Details | M-CSA 881 |
| Chain | Residue | Details |
| D | SER103 | proton shuttle (general acid/base) |
| D | CYS281 | covalent catalysis |
| D | HIS319 | metal ligand |
| D | ALA321 | metal ligand |
| D | GLN324 | metal ligand |
| D | ASN350 | metal ligand |
