5JYX
Crystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008033 | biological_process | tRNA processing |
| A | 0008616 | biological_process | queuosine biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0033739 | molecular_function | preQ1 synthase activity |
| B | 0008033 | biological_process | tRNA processing |
| B | 0008616 | biological_process | queuosine biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0033739 | molecular_function | preQ1 synthase activity |
| C | 0008033 | biological_process | tRNA processing |
| C | 0008616 | biological_process | queuosine biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0033739 | molecular_function | preQ1 synthase activity |
| D | 0008033 | biological_process | tRNA processing |
| D | 0008616 | biological_process | queuosine biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0033739 | molecular_function | preQ1 synthase activity |
| E | 0008033 | biological_process | tRNA processing |
| E | 0008616 | biological_process | queuosine biosynthetic process |
| E | 0016740 | molecular_function | transferase activity |
| E | 0033739 | molecular_function | preQ1 synthase activity |
| F | 0008033 | biological_process | tRNA processing |
| F | 0008616 | biological_process | queuosine biosynthetic process |
| F | 0016740 | molecular_function | transferase activity |
| F | 0033739 | molecular_function | preQ1 synthase activity |
| G | 0008033 | biological_process | tRNA processing |
| G | 0008616 | biological_process | queuosine biosynthetic process |
| G | 0016740 | molecular_function | transferase activity |
| G | 0033739 | molecular_function | preQ1 synthase activity |
| H | 0008033 | biological_process | tRNA processing |
| H | 0008616 | biological_process | queuosine biosynthetic process |
| H | 0016740 | molecular_function | transferase activity |
| H | 0033739 | molecular_function | preQ1 synthase activity |
| I | 0008033 | biological_process | tRNA processing |
| I | 0008616 | biological_process | queuosine biosynthetic process |
| I | 0016740 | molecular_function | transferase activity |
| I | 0033739 | molecular_function | preQ1 synthase activity |
| J | 0008033 | biological_process | tRNA processing |
| J | 0008616 | biological_process | queuosine biosynthetic process |
| J | 0016740 | molecular_function | transferase activity |
| J | 0033739 | molecular_function | preQ1 synthase activity |
| K | 0008033 | biological_process | tRNA processing |
| K | 0008616 | biological_process | queuosine biosynthetic process |
| K | 0016740 | molecular_function | transferase activity |
| K | 0033739 | molecular_function | preQ1 synthase activity |
| L | 0008033 | biological_process | tRNA processing |
| L | 0008616 | biological_process | queuosine biosynthetic process |
| L | 0016740 | molecular_function | transferase activity |
| L | 0033739 | molecular_function | preQ1 synthase activity |
| M | 0008033 | biological_process | tRNA processing |
| M | 0008616 | biological_process | queuosine biosynthetic process |
| M | 0016740 | molecular_function | transferase activity |
| M | 0033739 | molecular_function | preQ1 synthase activity |
| N | 0008033 | biological_process | tRNA processing |
| N | 0008616 | biological_process | queuosine biosynthetic process |
| N | 0016740 | molecular_function | transferase activity |
| N | 0033739 | molecular_function | preQ1 synthase activity |
| O | 0008033 | biological_process | tRNA processing |
| O | 0008616 | biological_process | queuosine biosynthetic process |
| O | 0016740 | molecular_function | transferase activity |
| O | 0033739 | molecular_function | preQ1 synthase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 10 |
| Details | binding site for residue GD1 A 201 |
| Chain | Residue |
| A | CYS21 |
| C | GLU46 |
| A | ASP28 |
| A | LEU61 |
| A | HIS62 |
| A | GLU63 |
| A | TYR90 |
| C | VAL42 |
| C | LEU43 |
| C | ILE45 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue NA C 202 |
| Chain | Residue |
| C | GLU31 |
| C | SER33 |
| C | THR85 |
| C | HOH308 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue NA E 202 |
| Chain | Residue |
| E | GLU31 |
| E | SER33 |
| E | THR85 |
| E | HOH305 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | binding site for residue NA L 202 |
| Chain | Residue |
| L | SER33 |
| site_id | AC5 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 B 201 and CYS B 21 |
| Chain | Residue |
| B | VAL20 |
| B | PRO22 |
| B | ILE23 |
| B | SER24 |
| B | LYS25 |
| B | THR26 |
| B | ASP28 |
| B | LEU61 |
| B | HIS62 |
| B | GLU63 |
| B | TYR90 |
| E | LEU43 |
| E | ILE45 |
| E | GLU46 |
| site_id | AC6 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 C 201 and CYS C 21 |
| Chain | Residue |
| C | VAL20 |
| C | PRO22 |
| C | ILE23 |
| C | SER24 |
| C | LYS25 |
| C | THR26 |
| C | ASP28 |
| C | LEU61 |
| C | HIS62 |
| C | GLU63 |
| C | TYR90 |
| J | LEU43 |
| J | ILE45 |
| J | GLU46 |
| site_id | AC7 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide GD1 D 201 and CYS D 21 |
| Chain | Residue |
| D | VAL20 |
| D | PRO22 |
| D | ILE23 |
| D | SER24 |
| D | LYS25 |
| D | THR26 |
| D | ASP28 |
| D | LEU61 |
| D | HIS62 |
| D | GLU63 |
| D | TYR90 |
| H | VAL42 |
| H | LEU43 |
| H | ILE45 |
| H | GLU46 |
| site_id | AC8 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 E 201 and CYS E 21 |
| Chain | Residue |
| E | VAL20 |
| E | PRO22 |
| E | ILE23 |
| E | SER24 |
| E | LYS25 |
| E | THR26 |
| E | ASP28 |
| E | LEU61 |
| E | HIS62 |
| E | GLU63 |
| E | TYR90 |
| F | LEU43 |
| F | ILE45 |
| F | GLU46 |
| site_id | AC9 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide GD1 F 201 and CYS F 21 |
| Chain | Residue |
| F | VAL20 |
| F | PRO22 |
| F | ILE23 |
| F | SER24 |
| F | LYS25 |
| F | THR26 |
| F | ASP28 |
| F | LEU61 |
| F | HIS62 |
| F | GLU63 |
| F | TYR90 |
| O | LEU43 |
| O | ALA44 |
| O | ILE45 |
| O | GLU46 |
| site_id | AD1 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 G 201 and CYS G 21 |
| Chain | Residue |
| G | LYS25 |
| G | THR26 |
| G | ASP28 |
| G | HIS62 |
| G | GLU63 |
| G | TYR90 |
| D | VAL42 |
| D | LEU43 |
| D | ILE45 |
| D | GLU46 |
| G | VAL20 |
| G | PRO22 |
| G | ILE23 |
| G | SER24 |
| site_id | AD2 |
| Number of Residues | 16 |
| Details | binding site for Di-peptide GD1 H 201 and CYS H 21 |
| Chain | Residue |
| H | VAL20 |
| H | PRO22 |
| H | ILE23 |
| H | SER24 |
| H | LYS25 |
| H | THR26 |
| H | ASP28 |
| H | LEU61 |
| H | HIS62 |
| H | GLU63 |
| H | TYR90 |
| L | VAL42 |
| L | LEU43 |
| L | ALA44 |
| L | ILE45 |
| L | GLU46 |
| site_id | AD3 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide GD1 I 201 and CYS I 21 |
| Chain | Residue |
| B | VAL42 |
| B | LEU43 |
| B | ILE45 |
| B | GLU46 |
| I | VAL20 |
| I | PRO22 |
| I | ILE23 |
| I | SER24 |
| I | LYS25 |
| I | THR26 |
| I | ASP28 |
| I | LEU61 |
| I | HIS62 |
| I | GLU63 |
| I | TYR90 |
| site_id | AD4 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 J 201 and CYS J 21 |
| Chain | Residue |
| J | VAL20 |
| J | PRO22 |
| J | ILE23 |
| J | SER24 |
| J | LYS25 |
| J | THR26 |
| J | ASP28 |
| J | LEU61 |
| J | HIS62 |
| J | GLU63 |
| J | TYR90 |
| N | LEU43 |
| N | ILE45 |
| N | GLU46 |
| site_id | AD5 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 K 201 and CYS K 21 |
| Chain | Residue |
| G | LEU43 |
| G | ILE45 |
| G | GLU46 |
| K | VAL20 |
| K | PRO22 |
| K | ILE23 |
| K | SER24 |
| K | LYS25 |
| K | THR26 |
| K | ASP28 |
| K | LEU61 |
| K | HIS62 |
| K | GLU63 |
| K | TYR90 |
| site_id | AD6 |
| Number of Residues | 16 |
| Details | binding site for Di-peptide GD1 L 201 and CYS L 21 |
| Chain | Residue |
| K | LEU2 |
| K | LEU43 |
| K | ALA44 |
| K | ILE45 |
| K | GLU46 |
| L | VAL20 |
| L | PRO22 |
| L | ILE23 |
| L | SER24 |
| L | LYS25 |
| L | THR26 |
| L | ASP28 |
| L | LEU61 |
| L | HIS62 |
| L | GLU63 |
| L | TYR90 |
| site_id | AD7 |
| Number of Residues | 16 |
| Details | binding site for Di-peptide GD1 M 201 and CYS M 21 |
| Chain | Residue |
| A | VAL42 |
| A | LEU43 |
| A | ALA44 |
| A | ILE45 |
| A | GLU46 |
| M | VAL20 |
| M | PRO22 |
| M | ILE23 |
| M | SER24 |
| M | LYS25 |
| M | THR26 |
| M | ASP28 |
| M | LEU61 |
| M | HIS62 |
| M | GLU63 |
| M | TYR90 |
| site_id | AD8 |
| Number of Residues | 16 |
| Details | binding site for Di-peptide GD1 N 201 and CYS N 21 |
| Chain | Residue |
| M | LEU2 |
| M | VAL42 |
| M | LEU43 |
| M | ILE45 |
| M | GLU46 |
| N | VAL20 |
| N | PRO22 |
| N | ILE23 |
| N | SER24 |
| N | LYS25 |
| N | THR26 |
| N | ASP28 |
| N | LEU61 |
| N | HIS62 |
| N | GLU63 |
| N | TYR90 |
| site_id | AD9 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide GD1 O 201 and CYS O 21 |
| Chain | Residue |
| I | LEU43 |
| I | ILE45 |
| I | GLU46 |
| O | VAL20 |
| O | PRO22 |
| O | ILE23 |
| O | SER24 |
| O | LYS25 |
| O | THR26 |
| O | ASP28 |
| O | LEU61 |
| O | HIS62 |
| O | GLU63 |
| O | TYR90 |
Functional Information from PROSITE/UniProt
| site_id | PS00092 |
| Number of Residues | 7 |
| Details | N6_MTASE N-6 Adenine-specific DNA methylases signature. AAVNPPY |
| Chain | Residue | Details |
| A | ALA75-TYR81 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 15 |
| Details | ACT_SITE: Thioimide intermediate => ECO:0000269|PubMed:27802572, ECO:0000269|PubMed:28383498 |
| Chain | Residue | Details |
| A | CYS21 | |
| J | CYS21 | |
| K | CYS21 | |
| L | CYS21 | |
| M | CYS21 | |
| N | CYS21 | |
| O | CYS21 | |
| B | CYS21 | |
| C | CYS21 | |
| D | CYS21 | |
| E | CYS21 | |
| F | CYS21 | |
| G | CYS21 | |
| H | CYS21 | |
| I | CYS21 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 15 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000305|PubMed:27802572 |
| Chain | Residue | Details |
| A | ASP28 | |
| J | ASP28 | |
| K | ASP28 | |
| L | ASP28 | |
| M | ASP28 | |
| N | ASP28 | |
| O | ASP28 | |
| B | ASP28 | |
| C | ASP28 | |
| D | ASP28 | |
| E | ASP28 | |
| F | ASP28 | |
| G | ASP28 | |
| H | ASP28 | |
| I | ASP28 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 30 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:27802572 |
| Chain | Residue | Details |
| A | ASP28 | |
| E | HIS62 | |
| F | ASP28 | |
| F | HIS62 | |
| G | ASP28 | |
| G | HIS62 | |
| H | ASP28 | |
| H | HIS62 | |
| I | ASP28 | |
| I | HIS62 | |
| J | ASP28 | |
| A | HIS62 | |
| J | HIS62 | |
| K | ASP28 | |
| K | HIS62 | |
| L | ASP28 | |
| L | HIS62 | |
| M | ASP28 | |
| M | HIS62 | |
| N | ASP28 | |
| N | HIS62 | |
| O | ASP28 | |
| B | ASP28 | |
| O | HIS62 | |
| B | HIS62 | |
| C | ASP28 | |
| C | HIS62 | |
| D | ASP28 | |
| D | HIS62 | |
| E | ASP28 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 15 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27802572 |
| Chain | Residue | Details |
| A | LEU43 | |
| J | LEU43 | |
| K | LEU43 | |
| L | LEU43 | |
| M | LEU43 | |
| N | LEU43 | |
| O | LEU43 | |
| B | LEU43 | |
| C | LEU43 | |
| D | LEU43 | |
| E | LEU43 | |
| F | LEU43 | |
| G | LEU43 | |
| H | LEU43 | |
| I | LEU43 |
