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(-) Description

Title :  STRUCTURE OF THE TRUNCATED HUMAN DIHYDROLIPOYL ACETYLTRANSFERASE (E2)
 
Authors :  X. Yu, Y. Hiromasa, H. Tsen, J. K. Stoops, T. E. Roche, Z. H. Zhou
Date :  01 Nov 07  (Deposition) - 22 Jan 08  (Release) - 02 Feb 10  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  8.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Central Beta-Sheet Surrounded By Five Alpha-Helices, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yu, Y. Hiromasa, H. Tsen, J. K. Stoops, T. E. Roche, Z. H. Zhou
Structures Of The Human Pyruvate Dehydrogenase Complex Cores: A Highly Conserved Catalytic Center With Flexible N-Terminal Domains
Structure V. 16 104 2008
PubMed-ID: 18184588  |  Reference-DOI: 10.1016/J.STR.2007.10.024

(-) Compounds

Molecule 1 - DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE
    ChainsA
    EC Number2.3.1.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL CATALYTIC DOMAIN
    GeneDLAT, DLTA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCOMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL
    SynonymPYRUVATE DEHYDROGENASE COMPLEX E2 SUBUNIT;
PDCE2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3B8K)

(-) Sites  (0, 0)

(no "Site" information available for 3B8K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B8K)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr A:335 -Asp A:336
2Val A:416 -Ile A:417
3Ile A:417 -Arg A:418
4Asp A:521 -Val A:522
5Val A:522 -Ala A:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047416D451NODP2_HUMANPolymorphism10891314AD365N

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B8K)

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002803461aENSE00001130691chr11:111895538-111896475938ODP2_HUMAN1-93930--
1.2bENST000002803462bENSE00000996256chr11:111896922-111897023102ODP2_HUMAN94-127340--
1.3bENST000002803463bENSE00001105302chr11:111899239-111899363125ODP2_HUMAN128-169420--
1.4ENST000002803464ENSE00001128003chr11:111899516-111899669154ODP2_HUMAN169-220520--
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_HUMAN400-430311A:323-34422
1.10ENST0000028034610ENSE00001127959chr11:111916587-111916694108ODP2_HUMAN431-466361A:345-38036
1.11ENST0000028034611ENSE00000996257chr11:111921958-111922073116ODP2_HUMAN467-505391A:381-41939
1.12aENST0000028034612aENSE00000996239chr11:111930627-111930789163ODP2_HUMAN505-559551A:419-47355
1.13aENST0000028034613aENSE00000996255chr11:111931762-111931898137ODP2_HUMAN560-605461A:474-51946
1.14dENST0000028034614dENSE00001514061chr11:111933130-1119351141985ODP2_HUMAN605-647431A:519-56143

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:239
 aligned with ODP2_HUMAN | P10515 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:239
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638         
           ODP2_HUMAN   409 GPGMAPVPTGVFTDIPISNIRRVIAQRLMQSKQTIPHYYLSIDVNMGEVLLVRKELNKILEGRSKISVNDFIIKASALACLKVPEANSSWMDTVIRQNHVVDVSVAVSTPAGLITPIVFNAHIKGVETIANDVVSLATKAREGKLQPHEFQGGTFTISNLGMFGIKNFSAIINPPQACILAIGASEDKLVPADNEKGFDVASMMSVTLSCDHRVVDGAVGAQWLAEFRKYLEKPITMLL 647
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...................eee.ee....ee..ee......hhhhhhhhhhhhhhhhhh...hhhhhh...eeeee.....................ee.....................eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.9 [INCOMPLETE] Exon 1.10  PDB: A:345-380           Exon 1.11  PDB: A:381-419              ------------------------------------------------------Exon 1.13a  PDB: A:474-519 UniProt: 560-605   ------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------Exon 1.12a  PDB: A:419-473 UniProt: 505-559            ---------------------------------------------Exon 1.14d  PDB: A:519-561 UniProt: 605-647 Transcript 1 (2)
                 3b8k A 323 GPGMAPVPTGVFTDIPISNIRRVIAQRLMQSKQTIPHYYLSIDVNMGEVLLVRKELNKILEGRSKISVNDFIIKASALACLKVPEANSSWMDTVIRQNHVVDVSVAVSTPAGLITPIVFNAHIKGVETIANDVVSLATKAREGKLQPHEFQGGTFTISNLGMFGIKNFSAIINPPQACILAIGASEDKLVPADNEKGFDVASMMSVTLSCDHRVVDGAVGAQWLAEFRKYLEKPITMLL 561
                                   332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552         

   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  (0, 0)

(no "SCOP Domain" information available for 3B8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B8K)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(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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  Cis Peptide Bonds
    Asp A:521 - Val A:522   [ RasMol ]  
    Ile A:417 - Arg A:418   [ RasMol ]  
    Thr A:335 - Asp A:336   [ RasMol ]  
    Val A:416 - Ile A:417   [ RasMol ]  
    Val A:522 - Ala A:523   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1eaa ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX RELATED ID: EMD-1448 RELATED DB: EMDB