2GB5
Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000210 | molecular_function | NAD+ diphosphatase activity |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0006402 | biological_process | mRNA catabolic process |
| A | 0006734 | biological_process | NADH metabolic process |
| A | 0006742 | biological_process | NADP catabolic process |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0019677 | biological_process | NAD catabolic process |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0035529 | molecular_function | NADH pyrophosphatase activity |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048255 | biological_process | mRNA stabilization |
| A | 0110153 | molecular_function | RNA NAD-cap (NMN-forming) hydrolase activity |
| A | 0110155 | biological_process | NAD-cap decapping |
| B | 0000210 | molecular_function | NAD+ diphosphatase activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0006402 | biological_process | mRNA catabolic process |
| B | 0006734 | biological_process | NADH metabolic process |
| B | 0006742 | biological_process | NADP catabolic process |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0019677 | biological_process | NAD catabolic process |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0035529 | molecular_function | NADH pyrophosphatase activity |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0048255 | biological_process | mRNA stabilization |
| B | 0110153 | molecular_function | RNA NAD-cap (NMN-forming) hydrolase activity |
| B | 0110155 | biological_process | NAD-cap decapping |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 301 |
| Chain | Residue |
| A | CYS98 |
| A | CYS101 |
| A | CYS116 |
| A | CYS119 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 301 |
| Chain | Residue |
| B | CYS98 |
| B | CYS101 |
| B | CYS116 |
| B | CYS119 |
Functional Information from PROSITE/UniProt
| site_id | PS00893 |
| Number of Residues | 22 |
| Details | NUDIX_BOX Nudix box signature. GfvevgEtleqAVaREVmEEsG |
| Chain | Residue | Details |
| A | GLY159-GLY180 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27428510, ECO:0007744|PDB:5IW4 |
| Chain | Residue | Details |
| A | LYS25 | |
| B | LYS25 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27428510, ECO:0007744|PDB:5IW5 |
| Chain | Residue | Details |
| A | ARG69 | |
| B | ARG69 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27428510, ECO:0000269|PubMed:27561816, ECO:0000269|Ref.8, ECO:0007744|PDB:1VK6, ECO:0007744|PDB:2GB5, ECO:0007744|PDB:5ISY, ECO:0007744|PDB:5IW4, ECO:0007744|PDB:5IW5 |
| Chain | Residue | Details |
| B | CYS116 | |
| B | CYS119 | |
| A | CYS98 | |
| A | CYS101 | |
| A | CYS116 | |
| A | CYS119 | |
| B | CYS98 | |
| B | CYS101 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27561816, ECO:0007744|PDB:5ISY |
| Chain | Residue | Details |
| A | GLU111 | |
| B | GLU111 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27428510, ECO:0000269|PubMed:27561816, ECO:0007744|PDB:5ISY, ECO:0007744|PDB:5IW4 |
| Chain | Residue | Details |
| A | ALA241 | |
| B | TYR124 | |
| B | GLN192 | |
| B | ALA241 | |
| A | TYR124 | |
| A | GLN192 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q9DCN1 |
| Chain | Residue | Details |
| A | GLU178 | |
| A | GLU219 | |
| B | ALA158 | |
| B | GLU174 | |
| B | GLU178 | |
| B | GLU219 | |
| A | ALA158 | |
| A | GLU174 |
