1GZ3
Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003824 | molecular_function | catalytic activity |
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 | 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 | 0046872 | molecular_function | metal ion binding |
A | 0051287 | molecular_function | NAD binding |
A | 1902031 | biological_process | regulation of NADP metabolic process |
B | 0003824 | molecular_function | catalytic activity |
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 | 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 | 0046872 | molecular_function | metal ion binding |
B | 0051287 | molecular_function | NAD binding |
B | 1902031 | biological_process | regulation of NADP metabolic process |
C | 0003824 | molecular_function | catalytic activity |
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 | 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 | 0046872 | molecular_function | metal ion binding |
C | 0051287 | molecular_function | NAD binding |
C | 1902031 | biological_process | regulation of NADP metabolic process |
D | 0003824 | molecular_function | catalytic activity |
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 | 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 | 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 | 13 |
Details | BINDING SITE FOR RESIDUE OXL A 603 |
Chain | Residue |
A | ARG165 |
A | MN604 |
A | HOH2129 |
A | HOH2208 |
A | HOH2264 |
A | LEU167 |
A | LYS183 |
A | GLU255 |
A | ASP256 |
A | ASP279 |
A | ASN421 |
A | ASN466 |
A | ASN467 |
site_id | AC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN A 604 |
Chain | Residue |
A | ARG165 |
A | GLU255 |
A | ASP256 |
A | ASP279 |
A | OXL603 |
A | HOH2265 |
site_id | AC3 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE OXL B 603 |
Chain | Residue |
B | ARG165 |
B | LYS183 |
B | GLU255 |
B | ASP256 |
B | ASP279 |
B | ASN421 |
B | ASN466 |
B | ASN467 |
B | MN604 |
B | HOH2234 |
B | HOH2286 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN B 604 |
Chain | Residue |
B | ARG165 |
B | GLU255 |
B | ASP256 |
B | ASP279 |
B | OXL603 |
B | HOH2287 |
site_id | AC5 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE OXL C 603 |
Chain | Residue |
C | ARG165 |
C | LEU167 |
C | LYS183 |
C | GLU255 |
C | ASP256 |
C | ASP279 |
C | ASN421 |
C | ASN466 |
C | ASN467 |
C | MN604 |
C | HOH2249 |
C | HOH2293 |
C | HOH2298 |
site_id | AC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN C 604 |
Chain | Residue |
C | ARG165 |
C | GLU255 |
C | ASP256 |
C | ASP279 |
C | OXL603 |
C | HOH2299 |
site_id | AC7 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE OXL D 603 |
Chain | Residue |
D | ARG165 |
D | LEU167 |
D | LYS183 |
D | GLU255 |
D | ASP256 |
D | ASP279 |
D | ASN421 |
D | ASN466 |
D | ASN467 |
D | MN604 |
D | HOH2293 |
D | HOH2298 |
site_id | AC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN D 604 |
Chain | Residue |
D | ARG165 |
D | GLU255 |
D | ASP256 |
D | ASP279 |
D | OXL603 |
D | HOH2299 |
site_id | AC9 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE ATP A 601 |
Chain | Residue |
A | ARG165 |
A | LEU167 |
A | ASN259 |
A | ALA312 |
A | GLY313 |
A | GLU314 |
A | ALA315 |
A | ASP345 |
A | LYS346 |
A | VAL392 |
A | ALA393 |
A | GLY394 |
A | ALA395 |
A | LEU398 |
A | SER420 |
A | HOH2116 |
A | HOH2186 |
A | HOH2256 |
A | HOH2258 |
A | HOH2259 |
A | HOH2260 |
A | HOH2261 |
A | HOH2262 |
A | HOH2263 |
site_id | BC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FUM A 605 |
Chain | Residue |
A | ARG91 |
A | HOH2028 |
A | HOH2032 |
A | HOH2266 |
A | HOH2267 |
B | PHE127 |
A | GLN64 |
A | ARG67 |
site_id | BC2 |
Number of Residues | 24 |
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 | ALA395 |
B | LEU398 |
B | HOH2274 |
B | HOH2275 |
B | HOH2276 |
B | HOH2277 |
B | HOH2278 |
B | HOH2280 |
B | HOH2281 |
B | HOH2282 |
B | HOH2283 |
B | HOH2284 |
B | HOH2285 |
site_id | BC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FUM B 605 |
Chain | Residue |
A | PHE127 |
A | ARG128 |
B | GLN64 |
B | ARG67 |
B | ARG91 |
B | HOH2288 |
B | HOH2289 |
B | HOH2290 |
site_id | BC4 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE ATP C 601 |
Chain | Residue |
C | ARG165 |
C | ASN259 |
C | GLY311 |
C | ALA312 |
C | GLY313 |
C | GLU314 |
C | ALA315 |
C | ASP345 |
C | LYS346 |
C | VAL392 |
C | ALA393 |
C | GLY394 |
C | ALA395 |
C | SER420 |
C | HOH2136 |
C | HOH2152 |
C | HOH2289 |
C | HOH2290 |
C | HOH2291 |
C | HOH2292 |
C | HOH2293 |
C | HOH2294 |
C | HOH2295 |
C | HOH2296 |
C | HOH2297 |
site_id | BC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FUM C 605 |
Chain | Residue |
C | GLN64 |
C | ARG67 |
C | ARG91 |
C | HOH2037 |
C | HOH2043 |
C | HOH2300 |
D | PHE127 |
D | ARG128 |
site_id | BC6 |
Number of Residues | 24 |
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 | ALA395 |
D | LEU398 |
D | HOH2287 |
D | HOH2288 |
D | HOH2289 |
D | HOH2291 |
D | HOH2292 |
D | HOH2293 |
D | HOH2294 |
D | HOH2295 |
D | HOH2296 |
D | HOH2297 |
site_id | BC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FUM D 605 |
Chain | Residue |
C | PHE127 |
D | GLN64 |
D | ARG67 |
D | ILE88 |
D | ARG91 |
D | HOH2031 |
D | HOH2036 |
D | HOH2300 |
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, ECO:0007744|PDB:1GZ3, ECO:0007744|PDB:1GZ4, ECO:0007744|PDB:1PJ2, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJ4 |
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 | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJL, ECO:0007744|PDB:1QR6 |
Chain | Residue | Details |
A | ARG165 | |
A | ALA312 | |
B | ARG165 | |
B | ALA312 | |
C | ARG165 | |
C | ALA312 | |
D | ARG165 | |
D | ALA312 |
site_id | SWS_FT_FI5 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1GZ3, ECO:0007744|PDB:1GZ4, ECO:0007744|PDB:1PJ2, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJ4 |
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 | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1QR6 |
Chain | Residue | Details |
A | ASN259 | |
B | ASN259 | |
C | ASN259 | |
D | ASN259 |
site_id | SWS_FT_FI7 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1QR6 |
Chain | Residue | Details |
A | GLU314 | |
B | GLU314 | |
C | GLU314 | |
D | GLU314 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJL, ECO:0007744|PDB:1QR6 |
Chain | Residue | Details |
A | ALA315 | |
B | ALA315 | |
C | ALA315 | |
D | ALA315 |
site_id | SWS_FT_FI9 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1PJ2, ECO:0007744|PDB:1PJ4 |
Chain | Residue | Details |
A | ASN421 | |
A | ASN466 | |
B | ASN421 | |
B | ASN466 | |
C | ASN421 | |
C | ASN466 | |
D | ASN421 | |
D | ASN466 |
site_id | SWS_FT_FI10 |
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 |