7XDG
Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor MDSA
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004470 | molecular_function | malic enzyme activity |
| A | 0004471 | molecular_function | malate dehydrogenase (decarboxylating) (NAD+) activity |
| A | 0004473 | molecular_function | malate dehydrogenase (decarboxylating) (NADP+) activity |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0006090 | biological_process | pyruvate metabolic process |
| A | 0006108 | biological_process | malate metabolic process |
| A | 0008948 | molecular_function | oxaloacetate decarboxylase activity |
| A | 0009055 | molecular_function | electron transfer activity |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051287 | molecular_function | NAD binding |
| A | 1902031 | biological_process | regulation of NADP metabolic process |
| B | 0004470 | molecular_function | malic enzyme activity |
| B | 0004471 | molecular_function | malate dehydrogenase (decarboxylating) (NAD+) activity |
| B | 0004473 | molecular_function | malate dehydrogenase (decarboxylating) (NADP+) activity |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0006090 | biological_process | pyruvate metabolic process |
| B | 0006108 | biological_process | malate metabolic process |
| B | 0008948 | molecular_function | oxaloacetate decarboxylase activity |
| B | 0009055 | molecular_function | electron transfer activity |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051287 | molecular_function | NAD binding |
| B | 1902031 | biological_process | regulation of NADP metabolic process |
| C | 0004470 | molecular_function | malic enzyme activity |
| C | 0004471 | molecular_function | malate dehydrogenase (decarboxylating) (NAD+) activity |
| C | 0004473 | molecular_function | malate dehydrogenase (decarboxylating) (NADP+) activity |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005759 | cellular_component | mitochondrial matrix |
| C | 0006090 | biological_process | pyruvate metabolic process |
| C | 0006108 | biological_process | malate metabolic process |
| C | 0008948 | molecular_function | oxaloacetate decarboxylase activity |
| C | 0009055 | molecular_function | electron transfer activity |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| C | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0051287 | molecular_function | NAD binding |
| C | 1902031 | biological_process | regulation of NADP metabolic process |
| D | 0004470 | molecular_function | malic enzyme activity |
| D | 0004471 | molecular_function | malate dehydrogenase (decarboxylating) (NAD+) activity |
| D | 0004473 | molecular_function | malate dehydrogenase (decarboxylating) (NADP+) activity |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005759 | cellular_component | mitochondrial matrix |
| D | 0006090 | biological_process | pyruvate metabolic process |
| D | 0006108 | biological_process | malate metabolic process |
| D | 0008948 | molecular_function | oxaloacetate decarboxylase activity |
| D | 0009055 | molecular_function | electron transfer activity |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| D | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0051287 | molecular_function | NAD binding |
| D | 1902031 | biological_process | regulation of NADP metabolic process |
Functional Information from PROSITE/UniProt
| site_id | PS00331 |
| Number of Residues | 17 |
| Details | MALIC_ENZYMES Malic enzymes signature. FnDDiqGTAaVaLAGLL |
| Chain | Residue | Details |
| A | PHE276-LEU292 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000269|PubMed:12962632 |
| Chain | Residue | Details |
| A | TYR112 | |
| B | TYR112 | |
| C | TYR112 | |
| D | TYR112 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:12962632 |
| Chain | Residue | Details |
| A | LYS183 | |
| B | LYS183 | |
| C | LYS183 | |
| D | LYS183 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632 |
| Chain | Residue | Details |
| A | ARG67 | |
| A | ARG91 | |
| B | ARG67 | |
| B | ARG91 | |
| C | ARG67 | |
| C | ARG91 | |
| D | ARG67 | |
| D | ARG91 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12962632 |
| Chain | Residue | Details |
| A | ARG165 | |
| D | ARG165 | |
| D | ASN421 | |
| D | ASN466 | |
| A | ASN421 | |
| A | ASN466 | |
| B | ARG165 | |
| B | ASN421 | |
| B | ASN466 | |
| C | ARG165 | |
| C | ASN421 | |
| C | ASN466 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632 |
| Chain | Residue | Details |
| A | GLU255 | |
| D | GLU255 | |
| D | ASP256 | |
| D | ASP279 | |
| A | ASP256 | |
| A | ASP279 | |
| B | GLU255 | |
| B | ASP256 | |
| B | ASP279 | |
| C | GLU255 | |
| C | ASP256 | |
| C | ASP279 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12962632 |
| Chain | Residue | Details |
| A | ASN259 | |
| A | GLY311 | |
| B | ASN259 | |
| B | GLY311 | |
| C | ASN259 | |
| C | GLY311 | |
| D | ASN259 | |
| D | GLY311 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 20 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS156 | |
| B | LYS346 | |
| C | LYS156 | |
| C | LYS224 | |
| C | LYS240 | |
| C | LYS272 | |
| C | LYS346 | |
| D | LYS156 | |
| D | LYS224 | |
| D | LYS240 | |
| D | LYS272 | |
| A | LYS224 | |
| D | LYS346 | |
| A | LYS240 | |
| A | LYS272 | |
| A | LYS346 | |
| B | LYS156 | |
| B | LYS224 | |
| B | LYS240 | |
| B | LYS272 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 8 |
| Details | M-CSA 21 |
| Chain | Residue | Details |
| A | TYR112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ARG165 | electrostatic stabiliser, hydrogen bond donor |
| A | LYS183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| A | GLU255 | metal ligand |
| A | ASP256 | metal ligand |
| A | ASP278 | hydrogen bond acceptor, proton acceptor, proton donor |
| A | ASP279 | metal ligand |
| A | ASN421 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 8 |
| Details | M-CSA 21 |
| Chain | Residue | Details |
| B | TYR112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ARG165 | electrostatic stabiliser, hydrogen bond donor |
| B | LYS183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| B | GLU255 | metal ligand |
| B | ASP256 | metal ligand |
| B | ASP278 | hydrogen bond acceptor, proton acceptor, proton donor |
| B | ASP279 | metal ligand |
| B | ASN421 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA3 |
| Number of Residues | 8 |
| Details | M-CSA 21 |
| Chain | Residue | Details |
| C | TYR112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| C | ARG165 | electrostatic stabiliser, hydrogen bond donor |
| C | LYS183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| C | GLU255 | metal ligand |
| C | ASP256 | metal ligand |
| C | ASP278 | hydrogen bond acceptor, proton acceptor, proton donor |
| C | ASP279 | metal ligand |
| C | ASN421 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA4 |
| Number of Residues | 8 |
| Details | M-CSA 21 |
| Chain | Residue | Details |
| D | TYR112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| D | ARG165 | electrostatic stabiliser, hydrogen bond donor |
| D | LYS183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| D | GLU255 | metal ligand |
| D | ASP256 | metal ligand |
| D | ASP278 | hydrogen bond acceptor, proton acceptor, proton donor |
| D | ASP279 | metal ligand |
| D | ASN421 | electrostatic stabiliser, hydrogen bond donor |
