Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  INNERMOST LIPOYL DOMAIN OF THE PYRUVATE DEHYDROGENASE FROM ESCHERICHIA COLI
 
Authors :  D. D. Jones, M. J. Howard, R. N. Perham
Date :  29 Jun 99  (Deposition) - 30 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Dihydrolipoamide Acetyltransferase, Lipoyl Domain, Pyruvate Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. D. Jones, K. M. Scott, M. J. Howard, R. N. Perham
Restricted Motion Of The Lipoyl-Lysine Swinging Arm In The Pyruvate Dehydrogenase Complex Of Escherichia Coli
Biochemistry V. 39 8448 2000
PubMed-ID: 10913250  |  Reference-DOI: 10.1021/BI992978I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROLIPOAMIDE ACETYLTRANSFERASE
    Cellular Location: CYTOPLASM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: T7
    Fragment: LIPOAMIDE BINDING DOMAIN OF E2P
    Gene: E2P_ECOLI
    Organism Common: ESCHERICHIA COLI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Plasmid: PET11C
    Strain: BL21(DE3)

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QJO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QJO)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.ODP2_ECOLI2-75
105-178
206-279
  1-
-
A:2-75
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.ODP2_ECOLI25-54
128-157
229-258
  1-
-
A:25-54

(-) Exons   (0, 0)

(no "Exon" information available for 1QJO)

(-) 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:80
 aligned with ODP2_ECOLI | P06959 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:80
                                   214       224       234       244       254       264       274       284
           ODP2_ECOLI   205 GVKEVNVPDIGGDEVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVGDKVKTGSLIMIFEVEGAA 284
               SCOP domains d1qjoa_ A: Lipoyl domain of dihydrolipoamide acetyltransferase                   SCOP domains
               CATH domains 1qjoA00 A:1-80  [code=2.40.50.100, no name defined]                              CATH domains
               Pfam domains --Biotin_lipoyl-1qjoA01 A:3-74                                            ------ Pfam domains
         Sec.struct. author .eeeee........eeeeee.....eee.....eeeeee..eeeeee....eeeeeee....eee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -BIOTINYL_LIPOYL  PDB: A:2-75 UniProt: 206-279                             ----- PROSITE (1)
                PROSITE (2) ------------------------LIPOYL  PDB: A:25-54          -------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1qjo A   1 MVKEVNVPDIGGDEVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVGDKVKTGSLIMIFEVEGAA  80
                                    10        20        30        40        50        60        70        80

   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Hybrid (58)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (ODP2_ECOLI | P06959)
molecular function
    GO:0004742    dihydrolipoyllysine-residue acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + dihydrolipoamide = CoA + S-acetyldihydrolipoamide.
    GO:0031405    lipoic acid binding    Interacting selectively and non-covalently with lipoic acid, 1,2-dithiolane-3-pentanoic acid.
    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:0004738    pyruvate dehydrogenase activity    Catalysis of the oxidative decarboxylation of pyruvate.
    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:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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).

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1qjo)
 
  Sites
(no "Sites" information available for 1qjo)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qjo)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qjo
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ODP2_ECOLI | P06959
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ODP2_ECOLI | P06959
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ODP2_ECOLI | P06959: 2k7v

(-) Related Entries Specified in the PDB File

1dpc