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(-) Description

Title :  SOLUTION STRUCTURE OF THE LIPOIC ACID-BEARING DOMAIN OF THE E2 COMPONENT OF HUMAN, MITOCHONDRIAL BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE
 
Authors :  C. -F. Chang, H. -T. Chou, J. L. Chuang, D. T. Chuang, T. -H. Huang
Date :  24 Oct 01  (Deposition) - 14 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Lipoyl Acid Bearing, Human Bckd, Experimental Nmr Data, Average Structure, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. -F. Chang, H. -T. Chou, J. L. Chuang, D. T. Chuang, T. -H. Huang
Solution Structure And Dynamics Of The Lipoic Acid-Bearing Domain Of Human Mitochondrial Branched-Chain Alpha-Keto Acid Dehydrogenase Complex
J. Biol. Chem. V. 277 15865 2002
PubMed-ID: 11839747  |  Reference-DOI: 10.1074/JBC.M110952200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E2 COMPONENT OF BRANCHED-CHAIN AHPHA-KETOACID DEHYDROGENASE
    Chains: A
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: LIPOIC ACID-BEARING DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DIHYDROLIPOAMIDE BRANCHED CHAIN TRANSACYLASE

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1K8M)

(-) Sites  (0, 0)

(no "Site" information available for 1K8M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_015099I98MODB2_HUMANDisease (MSUD2)  ---AI38M
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.ODB2_HUMAN64-139  1A:4-79
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.ODB2_HUMAN89-118  1A:29-58

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003701321aENSE00001451903chr1:100715390-10071532665ODB2_HUMAN1-17170--
1.2ENST000003701322ENSE00000831299chr1:100706440-100706317124ODB2_HUMAN18-59420--
1.3ENST000003701323ENSE00000831298chr1:100701067-10070099276ODB2_HUMAN59-84261A:1-2424
1.4ENST000003701324ENSE00000831297chr1:100696470-100696289182ODB2_HUMAN84-145621A:24-8562
1.5ENST000003701325ENSE00000831296chr1:100684303-100684182122ODB2_HUMAN145-185411A:85-873
1.6ENST000003701326ENSE00000831295chr1:100681755-100681539217ODB2_HUMAN186-258730--
1.7ENST000003701327ENSE00000831294chr1:100680539-100680373167ODB2_HUMAN258-313560--
1.8bENST000003701328bENSE00000831293chr1:100676327-10067625078ODB2_HUMAN314-339260--
1.9ENST000003701329ENSE00000831292chr1:100672192-100672001192ODB2_HUMAN340-403640--
1.10ENST0000037013210ENSE00000831291chr1:100671857-10067178672ODB2_HUMAN404-427240--
1.11ENST0000037013211ENSE00001451905chr1:100661978-1006597362243ODB2_HUMAN428-482550--

(-) 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:87
 aligned with ODB2_HUMAN | P11182 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:87
                                    70        80        90       100       110       120       130       140       
           ODB2_HUMAN    61 RGQVVQFKLSDIGEGIREVTVKEWYVKEGDTVSQFDSICEVQSDKASVTITSRYDGVIKKLYYNLDDIAYVGKPLVDIETEALKDSE 147
               SCOP domains d1k8ma_ A:                                                                              SCOP domains
               CATH domains 1k8mA00 A:1-87  [code=2.40.50.100, no name defined]                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..........eeeeee......ee......eeee....eee......eeeeee......ee....eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------M------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---BIOTINYL_LIPOYL  PDB: A:4-79 UniProt: 64-139                                -------- PROSITE (1)
                PROSITE (2) ----------------------------LIPOYL  PDB: A:29-58          ----------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:1-24   ------------------------------------------------------------1.5 Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.4  PDB: A:24-85 UniProt: 84-145                        -- Transcript 1 (2)
                 1k8m A   1 MGQVVQFKLSDIGEGIREVTVKEWYVKEGDTVSQFDSICEVQSDKASVTITSRYDGVIKKLYYNLDDIAYVGKPLVDIETEALKDLE  87
                                    10        20        30        40        50        60        70        80
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K8M)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (ODB2_HUMAN | P11182)
molecular function
    GO:0043754    dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity    Catalysis of the reaction: 2-methylpropanoyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6-(S-[2-methylpropanoyl]dihydrolipoyl)lysine.
    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).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009083    branched-chain amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    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.
cellular component
    GO:0005947    mitochondrial alpha-ketoglutarate dehydrogenase complex    Mitochondrial complex that possesses alpha-ketoglutarate dehydrogenase activity.
    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:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ODB2_HUMAN | P11182: 1k8o 1zwv 2coo 3rnm

(-) Related Entries Specified in the PDB File

5078 5078 CONTAINS CHEMICAL SHIFT LISTS EXCLUDING FIRST MET RESIDUE
1k8o 1K8O CONTAINS 20 SRUCTURES OF THE SAME PROTEIN.