4YPR
Crystal Structure of D144N MutY bound to its anti-substrate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000701 | molecular_function | purine-specific mismatch base pair DNA N-glycosylase activity |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0006281 | biological_process | DNA repair |
| A | 0006284 | biological_process | base-excision repair |
| A | 0006298 | biological_process | mismatch repair |
| A | 0006950 | biological_process | response to stress |
| A | 0006974 | biological_process | DNA damage response |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| A | 0019104 | molecular_function | DNA N-glycosylase activity |
| A | 0032357 | molecular_function | oxidized purine DNA binding |
| A | 0034039 | molecular_function | 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity |
| A | 0035485 | molecular_function | adenine/guanine mispair binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| B | 0000701 | molecular_function | purine-specific mismatch base pair DNA N-glycosylase activity |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0006281 | biological_process | DNA repair |
| B | 0006284 | biological_process | base-excision repair |
| B | 0006298 | biological_process | mismatch repair |
| B | 0006950 | biological_process | response to stress |
| B | 0006974 | biological_process | DNA damage response |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| B | 0019104 | molecular_function | DNA N-glycosylase activity |
| B | 0032357 | molecular_function | oxidized purine DNA binding |
| B | 0034039 | molecular_function | 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity |
| B | 0035485 | molecular_function | adenine/guanine mispair binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue SF4 A 400 |
| Chain | Residue |
| A | CYS198 |
| A | CYS205 |
| A | CYS208 |
| A | CYS214 |
| A | ALA222 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue SF4 B 400 |
| Chain | Residue |
| B | CYS198 |
| B | CYS205 |
| B | CYS208 |
| B | CYS214 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | binding site for Di-nucleotide DC D 5 and 8OG D 6 |
| Chain | Residue |
| A | GLN48 |
| A | THR49 |
| A | LEU86 |
| A | GLY87 |
| A | TYR88 |
| A | TYR89 |
| A | GLY260 |
| A | LEU261 |
| A | LEU262 |
| A | PHE307 |
| A | SER308 |
| A | HIS309 |
| C | DA17 |
| C | DG19 |
| D | DA4 |
| D | DT7 |
| site_id | AC4 |
| Number of Residues | 18 |
| Details | binding site for Di-nucleotide 8OG D 6 and DT D 7 |
| Chain | Residue |
| A | GLN48 |
| A | THR49 |
| A | GLY85 |
| A | LEU86 |
| A | GLY87 |
| A | TYR88 |
| A | TYR89 |
| A | LEU261 |
| A | LEU262 |
| A | HIS305 |
| A | ALA306 |
| A | PHE307 |
| A | SER308 |
| A | PRO345 |
| A | VAL346 |
| C | DA17 |
| D | DC5 |
| D | DG8 |
| site_id | AC5 |
| Number of Residues | 17 |
| Details | binding site for Di-nucleotide DC F 5 and 8OG F 6 |
| Chain | Residue |
| B | GLN48 |
| B | THR49 |
| B | LEU86 |
| B | GLY87 |
| B | TYR88 |
| B | TYR89 |
| B | GLY260 |
| B | LEU261 |
| B | LEU262 |
| B | PHE307 |
| B | SER308 |
| B | HIS309 |
| E | DA17 |
| E | DG19 |
| F | DA4 |
| F | DT7 |
| F | HOH101 |
| site_id | AC6 |
| Number of Residues | 19 |
| Details | binding site for Di-nucleotide 8OG F 6 and DT F 7 |
| Chain | Residue |
| B | GLN48 |
| B | THR49 |
| B | GLY85 |
| B | LEU86 |
| B | GLY87 |
| B | TYR88 |
| B | TYR89 |
| B | LEU261 |
| B | LEU262 |
| B | HIS305 |
| B | ALA306 |
| B | PHE307 |
| B | SER308 |
| B | PRO345 |
| B | VAL346 |
| E | DA17 |
| F | DC5 |
| F | DG8 |
| F | HOH101 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 56 |
| Details | Domain: {"description":"HhH","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"19841264","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19841264","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14961129","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19841264","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14961129","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19841264","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25995449","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2009","submissionDatabase":"PDB data bank","title":"Structural illumination of a mutY glycosylase reaction coordinate intermediate.","authors":["O'Shea V.L.","Cao S.","Richards J.L.","Horvath M.P.","David S.S."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2015","submissionDatabase":"PDB data bank","title":"Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.","authors":["Woods R.D.","O'Shea V.L.","Chu A.","Cao S.","Richards J.L.","Horvath M.P.","David S.S."]}},{"source":"PDB","id":"1RRQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RRS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1VRL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Site: {"description":"Transition state stabilizer","evidences":[{"source":"PubMed","id":"19841264","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25995449","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 3 |
| Details | M-CSA 807 |
| Chain | Residue | Details |
| A | GLU43 | activator, proton acceptor, proton donor |
| A | TYR126 | electrostatic stabiliser |
| A | ASN144 | covalently attached, nucleofuge, nucleophile |
| site_id | MCSA2 |
| Number of Residues | 3 |
| Details | M-CSA 807 |
| Chain | Residue | Details |
| B | GLU43 | activator, proton acceptor, proton donor |
| B | TYR126 | electrostatic stabiliser |
| B | ASN144 | covalently attached, nucleofuge, nucleophile |
