1GZ4
molecular mechanism of the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate
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 | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 604 |
| Chain | Residue |
| A | GLU255 |
| A | ASP256 |
| A | ASP279 |
| A | TTN603 |
| A | HOH2148 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN B 604 |
| Chain | Residue |
| B | TTN603 |
| B | HOH2138 |
| B | ARG165 |
| B | GLU255 |
| B | ASP256 |
| B | ASP279 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN C 604 |
| Chain | Residue |
| C | ARG165 |
| C | GLU255 |
| C | ASP256 |
| C | ASP279 |
| C | TTN603 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN D 604 |
| Chain | Residue |
| D | ARG165 |
| D | GLU255 |
| D | ASP256 |
| D | ASP279 |
| D | TTN603 |
| D | HOH2147 |
| site_id | AC5 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE ATP A 601 |
| Chain | Residue |
| A | ARG165 |
| A | ASN259 |
| 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 | SER420 |
| A | HOH2078 |
| A | HOH2143 |
| A | HOH2144 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE ATP A 602 |
| Chain | Residue |
| A | HIS154 |
| A | LYS156 |
| A | GLY192 |
| A | ILE193 |
| A | ARG194 |
| A | ARG197 |
| A | ILE479 |
| A | LEU480 |
| A | ASN482 |
| A | ARG542 |
| A | TYR552 |
| A | ARG556 |
| A | HOH2145 |
| site_id | AC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE TTN 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 | MN604 |
| A | HOH2146 |
| A | HOH2147 |
| site_id | AC8 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE FUM A 605 |
| Chain | Residue |
| A | GLN64 |
| A | ARG67 |
| A | ARG91 |
| A | LEU95 |
| A | HOH2023 |
| A | HOH2025 |
| A | HOH2149 |
| A | HOH2150 |
| B | PHE127 |
| B | ARG128 |
| B | HOH2030 |
| site_id | AC9 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE ATP B 601 |
| Chain | Residue |
| B | ARG165 |
| B | ASN259 |
| B | GLY311 |
| B | ALA312 |
| B | GLY313 |
| B | GLU314 |
| B | ALA315 |
| B | ASP345 |
| B | LYS346 |
| B | VAL392 |
| B | ALA393 |
| B | GLY394 |
| B | SER420 |
| B | HOH2130 |
| B | HOH2131 |
| B | HOH2132 |
| B | HOH2133 |
| B | HOH2134 |
| B | HOH2135 |
| B | HOH2136 |
| site_id | BC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE ATP B 602 |
| Chain | Residue |
| B | GLY192 |
| B | ILE193 |
| B | ARG194 |
| B | ARG197 |
| B | ILE479 |
| B | LEU480 |
| B | ARG542 |
| B | ARG556 |
| B | HOH2137 |
| B | HIS154 |
| B | LYS156 |
| site_id | BC2 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE TTN B 603 |
| Chain | Residue |
| B | TYR112 |
| B | ARG165 |
| B | LEU167 |
| B | LYS183 |
| B | GLU255 |
| B | ASP256 |
| B | ASP279 |
| B | ASN421 |
| B | ASN466 |
| B | ASN467 |
| B | MN604 |
| B | HOH2113 |
| B | HOH2136 |
| site_id | BC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE FUM B 605 |
| Chain | Residue |
| A | PHE127 |
| A | ARG128 |
| B | GLN64 |
| B | ARG67 |
| B | ARG91 |
| B | LEU95 |
| B | HOH2019 |
| B | HOH2139 |
| B | HOH2140 |
| B | HOH2141 |
| B | HOH2142 |
| site_id | BC4 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE ATP C 601 |
| Chain | Residue |
| C | ARG165 |
| C | LEU167 |
| C | ASN259 |
| C | ALA312 |
| C | GLY313 |
| C | GLU314 |
| C | ALA315 |
| C | ASP345 |
| C | LYS346 |
| C | VAL392 |
| C | ALA393 |
| C | GLY394 |
| C | ALA395 |
| C | SER420 |
| C | HOH2095 |
| C | HOH2125 |
| C | HOH2126 |
| C | HOH2127 |
| site_id | BC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE ATP C 602 |
| Chain | Residue |
| C | HIS154 |
| C | LYS156 |
| C | GLY192 |
| C | ILE193 |
| C | ARG194 |
| C | ARG197 |
| C | ILE479 |
| C | LEU480 |
| C | ARG542 |
| C | TYR552 |
| C | ARG556 |
| C | HOH2128 |
| site_id | BC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE TTN C 603 |
| Chain | Residue |
| C | TYR112 |
| C | ARG165 |
| C | LEU167 |
| C | LYS183 |
| C | GLU255 |
| C | ASP256 |
| C | ASP279 |
| C | ASN421 |
| C | ASN466 |
| C | ASN467 |
| C | MN604 |
| site_id | BC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FUM C 605 |
| Chain | Residue |
| C | GLN64 |
| C | ARG67 |
| C | ARG91 |
| C | LEU95 |
| C | HOH2015 |
| C | HOH2027 |
| C | HOH2129 |
| C | HOH2130 |
| D | PHE127 |
| D | ARG128 |
| site_id | BC8 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE ATP D 601 |
| Chain | Residue |
| D | ARG165 |
| D | ASN259 |
| D | GLY311 |
| D | ALA312 |
| D | GLY313 |
| D | GLU314 |
| D | ALA315 |
| D | ASP345 |
| D | LYS346 |
| D | VAL392 |
| D | ALA393 |
| D | GLY394 |
| D | LEU398 |
| D | SER420 |
| D | HOH2093 |
| D | HOH2139 |
| D | HOH2140 |
| D | HOH2141 |
| site_id | BC9 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE ATP D 602 |
| Chain | Residue |
| A | ASP244 |
| D | HIS154 |
| D | LYS156 |
| D | GLY192 |
| D | ILE193 |
| D | ARG194 |
| D | ARG197 |
| D | ILE479 |
| D | LEU480 |
| D | ASN482 |
| D | ARG542 |
| D | ARG556 |
| D | HOH2142 |
| D | HOH2143 |
| D | HOH2144 |
| site_id | CC1 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE TTN D 603 |
| Chain | Residue |
| D | TYR112 |
| D | ARG165 |
| D | LEU167 |
| D | LYS183 |
| D | GLU255 |
| D | ASP256 |
| D | ASP279 |
| D | ASN421 |
| D | ASN466 |
| D | ASN467 |
| D | MN604 |
| D | HOH2145 |
| D | HOH2146 |
| site_id | CC2 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE FUM D 605 |
| Chain | Residue |
| C | PHE127 |
| C | ARG128 |
| D | GLN64 |
| D | ARG67 |
| D | ARG91 |
| D | LEU95 |
| D | HOH2018 |
| D | HOH2022 |
| D | HOH2148 |
| D | HOH2149 |
| D | HOH2150 |
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 |
