2A8T
2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003729 | molecular_function | mRNA binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006402 | biological_process | mRNA catabolic process |
| A | 0008235 | molecular_function | metalloexopeptidase activity |
| A | 0009117 | biological_process | nucleotide metabolic process |
| A | 0016077 | biological_process | sno(s)RNA catabolic process |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0030515 | molecular_function | snoRNA binding |
| A | 0035863 | biological_process | dITP catabolic process |
| A | 0035870 | molecular_function | dITP diphosphatase activity |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050897 | molecular_function | cobalt ion binding |
| A | 0090068 | biological_process | positive regulation of cell cycle process |
| A | 0097383 | molecular_function | dIDP phosphatase activity |
| A | 0110152 | molecular_function | RNA NAD+-cap (NAD+-forming) hydrolase activity |
| A | 0110155 | biological_process | NAD-cap decapping |
| A | 0140933 | molecular_function | 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity |
| A | 1990003 | molecular_function | IDP phosphatase activity |
| A | 1990174 | molecular_function | phosphodiesterase decapping endonuclease activity |
| A | 2000233 | biological_process | negative regulation of rRNA processing |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0003729 | molecular_function | mRNA binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006402 | biological_process | mRNA catabolic process |
| B | 0008235 | molecular_function | metalloexopeptidase activity |
| B | 0009117 | biological_process | nucleotide metabolic process |
| B | 0016077 | biological_process | sno(s)RNA catabolic process |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0030515 | molecular_function | snoRNA binding |
| B | 0035863 | biological_process | dITP catabolic process |
| B | 0035870 | molecular_function | dITP diphosphatase activity |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050897 | molecular_function | cobalt ion binding |
| B | 0090068 | biological_process | positive regulation of cell cycle process |
| B | 0097383 | molecular_function | dIDP phosphatase activity |
| B | 0110152 | molecular_function | RNA NAD+-cap (NAD+-forming) hydrolase activity |
| B | 0110155 | biological_process | NAD-cap decapping |
| B | 0140933 | molecular_function | 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity |
| B | 1990003 | molecular_function | IDP phosphatase activity |
| B | 1990174 | molecular_function | phosphodiesterase decapping endonuclease activity |
| B | 2000233 | biological_process | negative regulation of rRNA processing |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 300 |
| Chain | Residue |
| A | GLY72 |
| A | GLU93 |
| A | MGT251 |
| A | MN301 |
| A | HOH633 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN A 301 |
| Chain | Residue |
| A | MN300 |
| A | MN303 |
| A | HOH505 |
| A | GLU89 |
| A | GLU93 |
| A | GLU150 |
| A | MGT251 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN A 302 |
| Chain | Residue |
| A | ARG88 |
| A | GLU89 |
| A | MGT251 |
| A | MN303 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN A 303 |
| Chain | Residue |
| A | GLU150 |
| A | MGT251 |
| A | MN301 |
| A | MN302 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN B 304 |
| Chain | Residue |
| B | GLY72 |
| B | GLU93 |
| B | MGT251 |
| B | MN305 |
| B | HOH635 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MN B 305 |
| Chain | Residue |
| B | GLY72 |
| B | GLU89 |
| B | GLU92 |
| B | GLU93 |
| B | ASP146 |
| B | GLU150 |
| B | MGT251 |
| B | MN304 |
| B | MN306 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN B 306 |
| Chain | Residue |
| B | GLU89 |
| B | GLU150 |
| B | MGT251 |
| B | MN305 |
| B | HOH615 |
| B | HOH628 |
| B | HOH629 |
| site_id | AC8 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE MGT A 251 |
| Chain | Residue |
| A | HIS37 |
| A | ARG63 |
| A | PHE64 |
| A | GLY72 |
| A | GLY73 |
| A | PHE74 |
| A | GLU89 |
| A | GLU93 |
| A | GLU150 |
| A | ADN252 |
| A | MN300 |
| A | MN301 |
| A | MN302 |
| A | MN303 |
| B | PHE49 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ADN A 252 |
| Chain | Residue |
| A | HIS37 |
| A | PHE74 |
| A | THR122 |
| A | ILE178 |
| A | ASN180 |
| A | SER181 |
| A | GLN184 |
| A | MGT251 |
| A | HOH639 |
| site_id | BC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE MGT B 251 |
| Chain | Residue |
| A | PHE49 |
| B | HIS37 |
| B | ARG63 |
| B | PHE64 |
| B | GLY72 |
| B | GLY73 |
| B | PHE74 |
| B | GLU89 |
| B | GLU93 |
| B | GLU150 |
| B | ADN252 |
| B | MN304 |
| B | MN305 |
| B | MN306 |
| B | HOH635 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ADN B 252 |
| Chain | Residue |
| B | HIS37 |
| B | PHE70 |
| B | PHE74 |
| B | THR122 |
| B | ILE178 |
| B | ASN180 |
| B | SER181 |
| B | GLN184 |
| B | MGT251 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 296 |
| Details | Domain: {"description":"Nudix hydrolase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 42 |
| Details | Motif: {"description":"Nudix box"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16472752","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"Q96DE0","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
