5J5Z
Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001669 | cellular_component | acrosomal vesicle |
| A | 0004148 | molecular_function | dihydrolipoyl dehydrogenase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0005929 | cellular_component | cilium |
| A | 0005967 | cellular_component | obsolete mitochondrial pyruvate dehydrogenase complex |
| A | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| A | 0006120 | biological_process | mitochondrial electron transport, NADH to ubiquinone |
| A | 0006508 | biological_process | proteolysis |
| A | 0007369 | biological_process | gastrulation |
| A | 0009083 | biological_process | branched-chain amino acid catabolic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016668 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor |
| A | 0031410 | cellular_component | cytoplasmic vesicle |
| A | 0031514 | cellular_component | motile cilium |
| A | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| A | 0042391 | biological_process | regulation of membrane potential |
| A | 0042995 | cellular_component | cell projection |
| A | 0043159 | cellular_component | acrosomal matrix |
| A | 0045240 | cellular_component | alpha-ketoacid dehydrogenase complex |
| A | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
| A | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| A | 0047101 | molecular_function | branched-chain alpha-keto acid dehydrogenase activity |
| A | 0048240 | biological_process | sperm capacitation |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| A | 0106077 | biological_process | obsolete histone succinylation |
| A | 1902493 | cellular_component | acetyltransferase complex |
| B | 0001669 | cellular_component | acrosomal vesicle |
| B | 0004148 | molecular_function | dihydrolipoyl dehydrogenase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0005929 | cellular_component | cilium |
| B | 0005967 | cellular_component | obsolete mitochondrial pyruvate dehydrogenase complex |
| B | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| B | 0006120 | biological_process | mitochondrial electron transport, NADH to ubiquinone |
| B | 0006508 | biological_process | proteolysis |
| B | 0007369 | biological_process | gastrulation |
| B | 0009083 | biological_process | branched-chain amino acid catabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016668 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor |
| B | 0031410 | cellular_component | cytoplasmic vesicle |
| B | 0031514 | cellular_component | motile cilium |
| B | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| B | 0042391 | biological_process | regulation of membrane potential |
| B | 0042995 | cellular_component | cell projection |
| B | 0043159 | cellular_component | acrosomal matrix |
| B | 0045240 | cellular_component | alpha-ketoacid dehydrogenase complex |
| B | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
| B | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| B | 0047101 | molecular_function | branched-chain alpha-keto acid dehydrogenase activity |
| B | 0048240 | biological_process | sperm capacitation |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0106077 | biological_process | obsolete histone succinylation |
| B | 1902493 | cellular_component | acetyltransferase complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 38 |
| Details | binding site for residue FAD A 501 |
| Chain | Residue |
| A | ILE12 |
| A | THR44 |
| A | CYS45 |
| A | VAL48 |
| A | GLY49 |
| A | CYS50 |
| A | LYS54 |
| A | GLY117 |
| A | TYR118 |
| A | GLY119 |
| A | ALA147 |
| A | GLY13 |
| A | THR148 |
| A | GLY149 |
| A | SER150 |
| A | ILE189 |
| A | ARG280 |
| A | PHE283 |
| A | GLY319 |
| A | ASP320 |
| A | MET326 |
| A | LEU327 |
| A | GLY15 |
| A | ALA328 |
| A | HIS329 |
| A | TYR359 |
| A | HOH649 |
| A | HOH667 |
| A | HOH668 |
| A | HOH696 |
| A | HOH788 |
| B | HIS452 |
| A | PRO16 |
| A | GLY17 |
| A | GLU36 |
| A | LYS37 |
| A | ASN38 |
| A | GLY43 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue PO4 A 502 |
| Chain | Residue |
| A | ARG299 |
| A | ARG301 |
| A | GLY324 |
| A | GOL504 |
| A | HOH622 |
| A | HOH797 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 503 |
| Chain | Residue |
| A | THR284 |
| A | ASN286 |
| A | LEU287 |
| A | GLY288 |
| A | LEU289 |
| A | GLU290 |
| A | GLU291 |
| A | HOH616 |
| A | HOH642 |
| A | HOH769 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 504 |
| Chain | Residue |
| A | ARG301 |
| A | GLN409 |
| A | SER411 |
| A | PO4502 |
| A | HOH644 |
| A | HOH658 |
| A | HOH676 |
| A | HOH845 |
| site_id | AC5 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 505 |
| Chain | Residue |
| A | ASP333 |
| A | HIS348 |
| A | ASP350 |
| A | CYS353 |
| A | GLU437 |
| A | HOH601 |
| A | HOH621 |
| A | HOH624 |
| B | ARG447 |
| site_id | AC6 |
| Number of Residues | 39 |
| Details | binding site for residue FAD B 501 |
| Chain | Residue |
| B | ASP320 |
| B | MET326 |
| B | LEU327 |
| B | ALA328 |
| B | HIS329 |
| B | TYR359 |
| B | HOH605 |
| B | HOH628 |
| B | HOH655 |
| B | HOH656 |
| B | HOH721 |
| A | HIS452 |
| B | ILE12 |
| B | GLY13 |
| B | GLY15 |
| B | PRO16 |
| B | GLY17 |
| B | ILE35 |
| B | GLU36 |
| B | LYS37 |
| B | ASN38 |
| B | GLY43 |
| B | THR44 |
| B | CYS45 |
| B | VAL48 |
| B | GLY49 |
| B | CYS50 |
| B | LYS54 |
| B | GLY117 |
| B | TYR118 |
| B | GLY119 |
| B | ALA147 |
| B | THR148 |
| B | GLY149 |
| B | SER150 |
| B | ILE189 |
| B | ARG280 |
| B | PHE283 |
| B | GLY319 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue PO4 B 502 |
| Chain | Residue |
| B | ARG299 |
| B | ARG301 |
| B | ALA323 |
| B | GLY324 |
Functional Information from PROSITE/UniProt
| site_id | PS00076 |
| Number of Residues | 11 |
| Details | PYRIDINE_REDOX_1 Pyridine nucleotide-disulphide oxidoreductases class-I active site. GGtCLnvGCIP |
| Chain | Residue | Details |
| A | GLY42-PRO52 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P09624 |
| Chain | Residue | Details |
| A | HIS452 | |
| B | HIS452 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15946682 |
| Chain | Residue | Details |
| A | GLU36 | |
| A | MET326 | |
| B | GLU36 | |
| B | LYS54 | |
| B | GLY119 | |
| B | THR148 | |
| B | GLY185 | |
| B | GLU208 | |
| B | VAL243 | |
| B | GLY279 | |
| B | ASP320 | |
| A | LYS54 | |
| B | MET326 | |
| A | GLY119 | |
| A | THR148 | |
| A | GLY185 | |
| A | GLU208 | |
| A | VAL243 | |
| A | GLY279 | |
| A | ASP320 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | SITE: Important for interaction with PDHX and activity of multienzyme pyruvate dehydrogenase complex => ECO:0000269|PubMed:20385101 |
| Chain | Residue | Details |
| A | ASP413 | |
| A | TYR438 | |
| B | ASP413 | |
| B | TYR438 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 14 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:O08749 |
| Chain | Residue | Details |
| A | LYS31 | |
| B | LYS87 | |
| B | LYS97 | |
| B | LYS108 | |
| B | LYS375 | |
| B | LYS470 | |
| A | LYS69 | |
| A | LYS87 | |
| A | LYS97 | |
| A | LYS108 | |
| A | LYS375 | |
| A | LYS470 | |
| B | LYS31 | |
| B | LYS69 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 10 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O08749 |
| Chain | Residue | Details |
| A | LYS124 | |
| B | LYS395 | |
| A | LYS131 | |
| A | LYS238 | |
| A | LYS242 | |
| A | LYS395 | |
| B | LYS124 | |
| B | LYS131 | |
| B | LYS238 | |
| B | LYS242 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O08749 |
| Chain | Residue | Details |
| A | SER250 | |
| B | SER250 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q6P6R2 |
| Chain | Residue | Details |
| A | SER262 | |
| B | SER262 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O08749 |
| Chain | Residue | Details |
| A | LYS311 | |
| A | LYS385 | |
| B | LYS311 | |
| B | LYS385 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS382 | |
| B | LYS382 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER467 | |
| B | SER467 |
