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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-058, A LIPOYL DOMAIN OF HUMAN 2-OXOACID DEHYDROGENASE
 
Authors :  A. Z. M. Ruhul Momen, H. Hirota, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 06  (Deposition) - 26 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lipoyl Domain, Lipoic Acid, 2-Oxoacid Dehydrogenase, Oxoacid Dehydrogenase, Synthesis Of Acyl Coa, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Z. M. Ruhul Momen, H. Hirota, F. Hayashi, S. Yokoyama
Solution Structure Of Rsgi Ruh-058, A Lipoyl Domain Of Human 2-Oxoacid Dehydrogenase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX
    ChainsA
    EC Number2.3.1.12
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050829-14
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN OF 2-OXOACID DEHYDROGENASE, LIPOYL-BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPYRUVATE DEHYDROGENASE COMPLEX E2 SUBUNIT, PDCE2, E2, DIHYDROLIPOAMIDE S-ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, PDC-E2, 70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS, PBC, M2 ANTIGEN COMPLEX 70 KDA SUBUNIT

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DNE)

(-) Sites  (0, 0)

(no "Site" information available for 2DNE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DNE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DNE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047411S98FODP2_HUMANPolymorphism537057AS14F
2UniProtVAR_047412L99FODP2_HUMANPolymorphism537060AL15F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.ODP2_HUMAN91-167
218-294
  1A:8-83
-
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.ODP2_HUMAN116-145
243-272
  1A:32-61
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002803461aENSE00001130691chr11:111895538-111896475938ODP2_HUMAN1-93931A:1-9 (gaps)28
1.2bENST000002803462bENSE00000996256chr11:111896922-111897023102ODP2_HUMAN94-127341A:10-4334
1.3bENST000002803463bENSE00001105302chr11:111899239-111899363125ODP2_HUMAN128-169421A:44-8542
1.4ENST000002803464ENSE00001128003chr11:111899516-111899669154ODP2_HUMAN169-220521A:85-10824
1.5aENST000002803465aENSE00001127996chr11:111904128-111904254127ODP2_HUMAN221-263430--
1.6ENST000002803466ENSE00001127990chr11:111907997-111908184188ODP2_HUMAN263-325630--
1.7aENST000002803467aENSE00001127984chr11:111909968-111910121154ODP2_HUMAN326-377520--
1.8ENST000002803468ENSE00001127976chr11:111914190-11191425768ODP2_HUMAN377-399230--
1.9ENST000002803469ENSE00001127968chr11:111915862-11191595493ODP2_HUMAN400-430310--
1.10ENST0000028034610ENSE00001127959chr11:111916587-111916694108ODP2_HUMAN431-466360--
1.11ENST0000028034611ENSE00000996257chr11:111921958-111922073116ODP2_HUMAN467-505390--
1.12aENST0000028034612aENSE00000996239chr11:111930627-111930789163ODP2_HUMAN505-559550--
1.13aENST0000028034613aENSE00000996255chr11:111931762-111931898137ODP2_HUMAN560-605460--
1.14dENST0000028034614dENSE00001514061chr11:111933130-1119351141985ODP2_HUMAN605-647430--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:108
 aligned with ODP2_HUMAN | P10515 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:127
                                    75        85        95       105       115       125       135       145       155       165       175       185       
           ODP2_HUMAN    66 GATPRNRLLLQLLGSPGRRYYSLPPHQKVPLPSLSPTMQAGTIARWEKKEGDKINEGDLIAEVETDKATVGFESLEECYMAKILVAEGTRDVPIGAIICITVGKPEDIEAFKNYTLDSSAAPTPQAA 192
               SCOP domains d2d          nea_          A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------....---------eeee.........eeeeee.......ee....eeeeee....eeeee....eeeee.........ee...eeeeee.hhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------FF--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------BIOTINYL_LIPOYL  PDB: A:8-83 UniProt: 91-167                                 ------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------LIPOYL  PDB: A:32-61          ----------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-9 (gaps)Exon 1.2b  PDB: A:10-43           Exon 1.3b  PDB: A:44-85 UniProt: 128-169  ----------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:85-108  Transcript 1 (2)
                 2dne A   1 GSS----------GSSG---------QKVPLPSLSPTMQAGTIARWEKKEGDKINEGDLIAEVETDKATVGFESLEECYMAKILVAEGTRDVPIGAIICITVGKPEDIEAFKNYTLDSSAASGPSSG 108
                              |      -   |  |  -      | 11        21        31        41        51        61        71        81        91       101       
                              3          4  7         8                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DNE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DNE)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (ODP2_HUMAN | P10515)
molecular function
    GO:0004742    dihydrolipoyllysine-residue acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + dihydrolipoamide = CoA + S-acetyldihydrolipoamide.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0034604    pyruvate dehydrogenase (NAD+) activity    Catalysis of the reaction: pyruvate + CoA + NAD+ = acetyl-CoA + CO2 + NADH.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006086    acetyl-CoA biosynthetic process from pyruvate    The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0046487    glyoxylate metabolic process    The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
    GO:0010510    regulation of acetyl-CoA biosynthetic process from pyruvate    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.
    GO:0030431    sleep    Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005967    mitochondrial pyruvate dehydrogenase complex    Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA in eukaryotes; includes subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The This Eukaryotic form usually contains more subunits than its bacterial counterpart; for example, one known complex contains 30 E1 dimers, 60 E2 monomers, and 6 E3 dimers as well as a few copies of pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0045254    pyruvate dehydrogenase complex    Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ODP2_HUMAN | P105151fyc 1y8n 1y8o 1y8p 2pnr 2q8i 3b8k 3crk 3crl

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