1EFK
STRUCTURE OF HUMAN MALIC ENZYME IN COMPLEX WITH KETOMALONATE
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 PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 604 |
| Chain | Residue |
| A | ARG165 |
| A | GLU255 |
| A | ASP256 |
| A | ASP279 |
| A | MAK603 |
| A | HOH4072 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 1604 |
| Chain | Residue |
| B | ASP279 |
| B | MAK1603 |
| B | HOH4073 |
| B | ARG165 |
| B | GLU255 |
| B | ASP256 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG C 2604 |
| Chain | Residue |
| C | ARG165 |
| C | LYS183 |
| C | GLU255 |
| C | ASP256 |
| C | ASP279 |
| C | MAK2603 |
| C | HOH4074 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 3604 |
| Chain | Residue |
| D | ARG165 |
| D | GLU255 |
| D | ASP256 |
| D | ASP279 |
| D | MAK3603 |
| D | HOH4075 |
| site_id | AC5 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE NAD A 601 |
| Chain | Residue |
| A | ARG165 |
| A | LEU167 |
| A | GLY168 |
| A | ASN259 |
| A | ASP279 |
| A | THR283 |
| A | LEU310 |
| A | GLY311 |
| A | ALA312 |
| A | GLY313 |
| A | GLU314 |
| A | ALA315 |
| A | ASP345 |
| A | LYS346 |
| A | VAL392 |
| A | ALA393 |
| A | GLY394 |
| A | ALA395 |
| A | LEU419 |
| A | SER420 |
| A | ASN421 |
| A | GLY446 |
| A | GLY465 |
| A | ASN466 |
| A | ASN467 |
| A | MAK603 |
| A | HOH4006 |
| site_id | AC6 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE NAD A 602 |
| Chain | Residue |
| A | HIS154 |
| A | ARG194 |
| A | ARG197 |
| A | ILE479 |
| A | LEU480 |
| A | ASN482 |
| A | ARG542 |
| A | TYR552 |
| A | ARG556 |
| D | ASP244 |
| D | ARG245 |
| D | GLY247 |
| site_id | AC7 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE NAD B 1601 |
| Chain | Residue |
| B | ARG165 |
| B | LEU167 |
| B | GLY168 |
| B | ASN259 |
| B | ASP279 |
| B | THR283 |
| B | GLY311 |
| B | ALA312 |
| B | GLY313 |
| B | GLU314 |
| B | ALA315 |
| B | ASP345 |
| B | LYS346 |
| B | VAL392 |
| B | ALA393 |
| B | GLY394 |
| B | ALA395 |
| B | LEU398 |
| B | LEU419 |
| B | ASN421 |
| B | GLY446 |
| B | GLY465 |
| B | ASN466 |
| B | ASN467 |
| B | MAK1603 |
| site_id | AC8 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE NAD B 1602 |
| Chain | Residue |
| C | ARG245 |
| B | HIS154 |
| B | LYS156 |
| B | GLY192 |
| B | ILE193 |
| B | ARG194 |
| B | ARG197 |
| B | ILE479 |
| B | ARG542 |
| B | TYR552 |
| B | ARG556 |
| site_id | AC9 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE NAD C 2601 |
| Chain | Residue |
| C | ARG165 |
| C | LEU167 |
| C | GLY168 |
| C | ASN259 |
| C | ASP279 |
| C | THR283 |
| C | GLY311 |
| C | ALA312 |
| C | GLY313 |
| C | GLU314 |
| C | ALA315 |
| C | ASP345 |
| C | LYS346 |
| C | VAL392 |
| C | ALA393 |
| C | GLY394 |
| C | ALA395 |
| C | LEU419 |
| C | ASN421 |
| C | GLY446 |
| C | GLY465 |
| C | ASN466 |
| C | ASN467 |
| C | MAK2603 |
| site_id | BC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE NAD C 2602 |
| Chain | Residue |
| B | ASP244 |
| B | ARG245 |
| C | HIS154 |
| C | LYS156 |
| C | GLY192 |
| C | ILE193 |
| C | ARG194 |
| C | ARG197 |
| C | ILE479 |
| C | LEU480 |
| C | TYR552 |
| C | ARG556 |
| site_id | BC2 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE NAD D 3601 |
| Chain | Residue |
| D | ARG165 |
| D | LEU167 |
| D | GLY168 |
| D | ASN259 |
| D | ASP279 |
| D | THR283 |
| D | LEU310 |
| D | GLY311 |
| D | ALA312 |
| D | GLY313 |
| D | GLU314 |
| D | ALA315 |
| D | ASP345 |
| D | LYS346 |
| D | VAL392 |
| D | ALA393 |
| D | GLY394 |
| D | ALA395 |
| D | LEU398 |
| D | LEU419 |
| D | ASN421 |
| D | GLY465 |
| D | ASN466 |
| D | ASN467 |
| D | MAK3603 |
| site_id | BC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE NAD D 3602 |
| Chain | Residue |
| A | ASP244 |
| A | ARG245 |
| D | HIS154 |
| D | ARG194 |
| D | ARG197 |
| D | ILE479 |
| D | LEU480 |
| D | ASN482 |
| D | ARG542 |
| D | TYR552 |
| D | ARG556 |
| site_id | BC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE MAK A 603 |
| Chain | Residue |
| A | TYR112 |
| A | ARG165 |
| A | LEU167 |
| A | LYS183 |
| A | GLU255 |
| A | ASP256 |
| A | ASP279 |
| A | ASN421 |
| A | ASN466 |
| A | ASN467 |
| A | NAD601 |
| A | MG604 |
| A | HOH4072 |
| site_id | BC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE MAK B 1603 |
| Chain | Residue |
| B | ARG165 |
| B | LEU167 |
| B | LYS183 |
| B | GLU255 |
| B | ASP256 |
| B | ASP279 |
| B | ASN421 |
| B | ASN466 |
| B | ASN467 |
| B | NAD1601 |
| B | MG1604 |
| B | HOH4073 |
| site_id | BC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE MAK C 2603 |
| Chain | Residue |
| C | TYR112 |
| C | ARG165 |
| C | LEU167 |
| C | LYS183 |
| C | GLU255 |
| C | ASP256 |
| C | ASP279 |
| C | ASN421 |
| C | ASN466 |
| C | ASN467 |
| C | NAD2601 |
| C | MG2604 |
| C | HOH4074 |
| site_id | BC7 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE MAK D 3603 |
| Chain | Residue |
| D | ARG165 |
| D | LEU167 |
| D | GLU255 |
| D | ASP256 |
| D | ASP279 |
| D | ASN421 |
| D | ASN466 |
| D | ASN467 |
| D | NAD3601 |
| D | MG3604 |
| D | HOH4075 |
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 | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1do8 |
| Chain | Residue | Details |
| A | ASP278 | |
| A | LYS183 | |
| A | TYR112 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1do8 |
| Chain | Residue | Details |
| B | ASP278 | |
| B | LYS183 | |
| B | TYR112 |
| site_id | CSA3 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1do8 |
| Chain | Residue | Details |
| C | ASP278 | |
| C | LYS183 | |
| C | TYR112 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1do8 |
| Chain | Residue | Details |
| D | ASP278 | |
| D | LYS183 | |
| D | TYR112 |
| 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 |
