1PJ3
Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate pyruvate, cofactor NAD+, Mn++, and allosteric activator 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 | PYR603 |
A | HOH4903 |
site_id | AC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN B 1604 |
Chain | Residue |
B | PYR1603 |
B | HOH4902 |
B | ARG1165 |
B | GLU1255 |
B | ASP1256 |
B | ASP1279 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN C 2604 |
Chain | Residue |
C | ARG2165 |
C | GLU2255 |
C | ASP2256 |
C | ASP2279 |
C | PYR2603 |
C | HOH4904 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN D 3604 |
Chain | Residue |
D | ARG3165 |
D | GLU3255 |
D | ASP3256 |
D | ASP3279 |
D | PYR3603 |
D | HOH4001 |
site_id | AC5 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE PYR 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 | MN604 |
A | HOH5000 |
site_id | AC6 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE PYR B 1603 |
Chain | Residue |
B | TYR1112 |
B | ARG1165 |
B | LEU1167 |
B | LYS1183 |
B | GLU1255 |
B | ASP1256 |
B | ASP1279 |
B | ASN1421 |
B | ASN1466 |
B | ASN1467 |
B | NAD1601 |
B | MN1604 |
B | HOH4902 |
B | HOH4964 |
site_id | AC7 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE PYR C 2603 |
Chain | Residue |
C | TYR2112 |
C | ARG2165 |
C | LEU2167 |
C | LYS2183 |
C | GLU2255 |
C | ASP2256 |
C | ASP2279 |
C | ASN2421 |
C | ASN2466 |
C | ASN2467 |
C | NAD2601 |
C | MN2604 |
C | HOH4904 |
site_id | AC8 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE PYR D 3603 |
Chain | Residue |
D | TYR3112 |
D | ARG3165 |
D | LEU3167 |
D | LYS3183 |
D | GLU3255 |
D | ASP3256 |
D | ASP3279 |
D | ASN3421 |
D | ASN3466 |
D | ASN3467 |
D | NAD3601 |
D | MN3604 |
D | HOH4001 |
D | HOH5039 |
site_id | AC9 |
Number of Residues | 34 |
Details | BINDING SITE FOR RESIDUE NAD A 601 |
Chain | Residue |
A | GLY446 |
A | GLY465 |
A | ASN466 |
A | ASN467 |
A | PYR603 |
A | HOH4045 |
A | HOH4124 |
A | HOH4126 |
A | HOH4186 |
A | HOH4647 |
A | HOH4891 |
A | HOH5144 |
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 | LEU398 |
A | LEU419 |
A | SER420 |
A | ASN421 |
site_id | BC1 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE NAD A 602 |
Chain | Residue |
A | GLY192 |
A | ILE193 |
A | ARG194 |
A | ARG197 |
A | ILE479 |
A | LEU480 |
A | ASN482 |
A | ARG542 |
A | TYR552 |
A | ARG556 |
A | HOH4030 |
D | ASP3244 |
D | ARG3245 |
D | GLY3247 |
site_id | BC2 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAD B 1601 |
Chain | Residue |
B | ARG1165 |
B | LEU1167 |
B | GLY1168 |
B | ASN1259 |
B | ASP1279 |
B | THR1283 |
B | GLY1311 |
B | ALA1312 |
B | GLY1313 |
B | GLU1314 |
B | ALA1315 |
B | ASP1345 |
B | LYS1346 |
B | VAL1392 |
B | ALA1393 |
B | GLY1394 |
B | ALA1395 |
B | LEU1398 |
B | LEU1419 |
B | SER1420 |
B | ASN1421 |
B | GLY1446 |
B | GLY1465 |
B | ASN1466 |
B | ASN1467 |
B | PYR1603 |
B | HOH4075 |
B | HOH4193 |
B | HOH4412 |
B | HOH4611 |
B | HOH4972 |
site_id | BC3 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE NAD B 1602 |
Chain | Residue |
B | HIS1154 |
B | LYS1156 |
B | GLY1192 |
B | ILE1193 |
B | ARG1194 |
B | ARG1197 |
B | ILE1479 |
B | LEU1480 |
B | ARG1542 |
B | TYR1552 |
B | ARG1556 |
C | ASP2244 |
C | GLY2247 |
C | HOH4569 |
site_id | BC4 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAD C 2601 |
Chain | Residue |
C | ARG2165 |
C | LEU2167 |
C | GLY2168 |
C | ASN2259 |
C | ASP2279 |
C | THR2283 |
C | LEU2310 |
C | ALA2312 |
C | GLY2313 |
C | GLU2314 |
C | ALA2315 |
C | ASP2345 |
C | LYS2346 |
C | VAL2392 |
C | ALA2393 |
C | GLY2394 |
C | ALA2395 |
C | LEU2419 |
C | SER2420 |
C | ASN2421 |
C | GLY2446 |
C | GLY2465 |
C | ASN2466 |
C | ASN2467 |
C | PYR2603 |
C | HOH4015 |
C | HOH4125 |
C | HOH4312 |
C | HOH4385 |
C | HOH4469 |
C | HOH4685 |
site_id | BC5 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE NAD C 2602 |
Chain | Residue |
B | ASP1244 |
B | ARG1245 |
B | GLY1247 |
C | HIS2154 |
C | LYS2156 |
C | GLY2192 |
C | ILE2193 |
C | ARG2194 |
C | ARG2197 |
C | ILE2479 |
C | LEU2480 |
C | ASN2482 |
C | ARG2542 |
C | TYR2552 |
C | ARG2556 |
C | HOH4556 |
site_id | BC6 |
Number of Residues | 30 |
Details | BINDING SITE FOR RESIDUE NAD D 3601 |
Chain | Residue |
D | ARG3165 |
D | LEU3167 |
D | GLY3168 |
D | ASN3259 |
D | ASP3279 |
D | THR3283 |
D | GLY3311 |
D | ALA3312 |
D | GLY3313 |
D | GLU3314 |
D | ALA3315 |
D | ASP3345 |
D | LYS3346 |
D | VAL3392 |
D | ALA3393 |
D | GLY3394 |
D | ALA3395 |
D | LEU3398 |
D | LEU3419 |
D | ASN3421 |
D | GLY3446 |
D | GLY3465 |
D | ASN3466 |
D | ASN3467 |
D | PYR3603 |
D | HOH4082 |
D | HOH4470 |
D | HOH4477 |
D | HOH4498 |
D | HOH5038 |
site_id | BC7 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE NAD D 3602 |
Chain | Residue |
A | ASP244 |
A | ARG245 |
A | GLY247 |
D | HIS3154 |
D | GLY3192 |
D | ILE3193 |
D | ARG3194 |
D | ARG3197 |
D | ILE3479 |
D | LEU3480 |
D | ASN3482 |
D | ARG3542 |
D | TYR3552 |
D | ARG3556 |
site_id | BC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE FUM A 700 |
Chain | Residue |
A | GLN64 |
A | ARG67 |
A | ARG91 |
A | HOH4071 |
A | HOH4374 |
A | HOH4394 |
B | PHE1127 |
B | ARG1128 |
B | HOH4198 |
site_id | BC9 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE FUM B 1700 |
Chain | Residue |
A | PHE127 |
B | GLN1064 |
B | ARG1067 |
B | ILE1088 |
B | ARG1091 |
B | LEU1095 |
B | HOH4031 |
B | HOH4038 |
B | HOH4094 |
B | HOH4139 |
B | HOH4332 |
site_id | CC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE FUM C 2700 |
Chain | Residue |
C | GLN2064 |
C | ARG2067 |
C | ARG2091 |
C | LEU2095 |
C | HOH4005 |
C | HOH4014 |
C | HOH4034 |
C | HOH4036 |
C | HOH4254 |
D | PHE3127 |
site_id | CC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE FUM D 3700 |
Chain | Residue |
C | PHE2127 |
D | GLN3064 |
D | ARG3067 |
D | ARG3091 |
D | HOH4035 |
D | HOH4059 |
D | HOH4081 |
D | HOH4098 |
D | HOH4119 |
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 | TYR1112 | |
C | TYR2112 | |
D | TYR3112 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:12962632 |
Chain | Residue | Details |
A | LYS183 | |
B | LYS1183 | |
C | LYS2183 | |
D | LYS3183 |
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 | ARG1067 | |
B | ARG1091 | |
C | ARG2067 | |
C | ARG2091 | |
D | ARG3067 | |
D | ARG3091 |
site_id | SWS_FT_FI4 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12962632 |
Chain | Residue | Details |
A | ARG165 | |
D | ARG3165 | |
D | ASN3421 | |
D | ASN3466 | |
A | ASN421 | |
A | ASN466 | |
B | ARG1165 | |
B | ASN1421 | |
B | ASN1466 | |
C | ARG2165 | |
C | ASN2421 | |
C | ASN2466 |
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 | GLU3255 | |
D | ASP3256 | |
D | ASP3279 | |
A | ASP256 | |
A | ASP279 | |
B | GLU1255 | |
B | ASP1256 | |
B | ASP1279 | |
C | GLU2255 | |
C | ASP2256 | |
C | ASP2279 |
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 | ASN1259 | |
B | GLY1311 | |
C | ASN2259 | |
C | GLY2311 | |
D | ASN3259 | |
D | GLY3311 |
site_id | SWS_FT_FI7 |
Number of Residues | 20 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
A | LYS156 | |
B | LYS1346 | |
C | LYS2156 | |
C | LYS2224 | |
C | LYS2240 | |
C | LYS2272 | |
C | LYS2346 | |
D | LYS3156 | |
D | LYS3224 | |
D | LYS3240 | |
D | LYS3272 | |
A | LYS224 | |
D | LYS3346 | |
A | LYS240 | |
A | LYS272 | |
A | LYS346 | |
B | LYS1156 | |
B | LYS1224 | |
B | LYS1240 | |
B | LYS1272 |
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 | LYS1183 | |
B | ASP1278 | |
B | TYR1112 |
site_id | CSA3 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1do8 |
Chain | Residue | Details |
C | ASP2278 | |
C | LYS2183 | |
C | TYR2112 |
site_id | CSA4 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1do8 |
Chain | Residue | Details |
D | ASP3278 | |
D | TYR3112 | |
D | LYS3183 |
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 | TYR1112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
B | ARG1165 | electrostatic stabiliser, hydrogen bond donor |
B | LYS1183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
B | GLU1255 | metal ligand |
B | ASP1256 | metal ligand |
B | ASP1278 | hydrogen bond acceptor, proton acceptor, proton donor |
B | ASP1279 | metal ligand |
B | ASN1421 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA3 |
Number of Residues | 8 |
Details | M-CSA 21 |
Chain | Residue | Details |
C | TYR2112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
C | ARG2165 | electrostatic stabiliser, hydrogen bond donor |
C | LYS2183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
C | GLU2255 | metal ligand |
C | ASP2256 | metal ligand |
C | ASP2278 | hydrogen bond acceptor, proton acceptor, proton donor |
C | ASP2279 | metal ligand |
C | ASN2421 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA4 |
Number of Residues | 8 |
Details | M-CSA 21 |
Chain | Residue | Details |
D | TYR3112 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
D | ARG3165 | electrostatic stabiliser, hydrogen bond donor |
D | LYS3183 | electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
D | GLU3255 | metal ligand |
D | ASP3256 | metal ligand |
D | ASP3278 | hydrogen bond acceptor, proton acceptor, proton donor |
D | ASP3279 | metal ligand |
D | ASN3421 | electrostatic stabiliser, hydrogen bond donor |