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{
"metadata": {
"accession": "cd05311",
"entry_id": null,
"type": "domain",
"go_terms": null,
"source_database": "cdd",
"member_databases": null,
"integrated": "IPR045213",
"hierarchy": null,
"name": {
"name": "NAD(P) binding domain of malic enzyme (ME), subgroup 2",
"short": "NAD_bind_2_malic_enz"
},
"description": [
{
"text": "<p>Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. [[cite:PUB00022087], [cite:PUB00033155], [cite:PUB00029877], [cite:PUB00024266], [cite:PUB00025336], [cite:PUB00113840]]</p>",
"llm": false,
"checked": false,
"updated": false
}
],
"wikipedia": null,
"literature": {
"PUB00033155": {
"PMID": 10467136,
"ISBN": null,
"volume": "7",
"issue": "8",
"year": 1999,
"title": "Crystal structure of human mitochondrial NAD(P)(+)-dependent malic enzyme: a new class of oxidative decarboxylases.",
"URL": null,
"raw_pages": "877-889",
"medline_journal": "Structure Fold Des",
"ISO_journal": "Structure Fold. Des.",
"authors": [
"Xu Y",
"Bhargava G",
"Wu H",
"Loeber G",
"Tong L."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0969-2126(99)80115-4"
},
"PUB00025336": {
"PMID": 11790843,
"ISBN": null,
"volume": "11",
"issue": "2",
"year": 2002,
"title": "Structural studies of the pigeon cytosolic NADP(+)-dependent malic enzyme.",
"URL": null,
"raw_pages": "332-41",
"medline_journal": "Protein Sci",
"ISO_journal": "Protein Sci.",
"authors": [
"Yang Z",
"Zhang H",
"Hung HC",
"Kuo CC",
"Tsai LC",
"Yuan HS",
"Chou WY",
"Chang GG",
"Tong L."
],
"DOI_URL": "http://dx.doi.org/10.1110/ps.38002"
},
"PUB00113840": {
"PMID": 11172800,
"ISBN": null,
"volume": "490",
"issue": "1-2",
"year": 2001,
"title": "NADP-malic enzyme from plants: a ubiquitous enzyme involved in different metabolic pathways.",
"URL": null,
"raw_pages": "1-6",
"medline_journal": "FEBS Lett",
"ISO_journal": "FEBS Lett",
"authors": [
"Drincovich MF",
"Casati P",
"Andreo CS."
],
"DOI_URL": null
},
"PUB00022087": {
"PMID": 12033925,
"ISBN": null,
"volume": "41",
"issue": "22",
"year": 2002,
"title": "Crystal structure of the malic enzyme from Ascaris suum complexed with nicotinamide adenine dinucleotide at 2.3 A resolution.",
"URL": null,
"raw_pages": "6928-38",
"medline_journal": "Biochemistry",
"ISO_journal": "Biochemistry",
"authors": [
"Coleman DE",
"Rao GS",
"Goldsmith EJ",
"Cook PF",
"Harris BG."
],
"DOI_URL": "http://dx.doi.org/10.1021/bi0255120"
},
"PUB00024266": {
"PMID": 10700286,
"ISBN": null,
"volume": "7",
"issue": "3",
"year": 2000,
"title": "Structure of a closed form of human malic enzyme and implications for catalytic mechanism.",
"URL": null,
"raw_pages": "251-7",
"medline_journal": "Nat Struct Biol",
"ISO_journal": "Nat. Struct. Biol.",
"authors": [
"Yang Z",
"Floyd DL",
"Loeber G",
"Tong L."
],
"DOI_URL": "http://dx.doi.org/10.1038/73378"
},
"PUB00029877": {
"PMID": 12962632,
"ISBN": null,
"volume": "11",
"issue": "9",
"year": 2003,
"title": "Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism.",
"URL": null,
"raw_pages": "1141-50",
"medline_journal": "Structure",
"ISO_journal": "Structure",
"authors": [
"Tao X",
"Yang Z",
"Tong L."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0969-2126(03)00168-0"
}
},
"set_info": {
"accession": "cl21454",
"name": "NADB_Rossmann"
},
"overlaps_with": null,
"counters": {
"subfamilies": 0,
"domain_architectures": 0,
"interactions": 0,
"matches": 26841,
"pathways": 0,
"proteins": 26835,
"proteomes": 14496,
"sets": 1,
"structural_models": {
"alphafold": 20110,
"bfvd": 0
},
"structures": 12,
"taxa": 23930
},
"entry_annotations": {},
"cross_references": {},
"is_llm": false,
"is_reviewed_llm": false,
"is_updated_llm": false,
"representative_structure": {
"accession": "6zn7",
"name": "MaeB malic enzyme domain apoprotein"
}
}
}
