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(-) Description

Title :  3D STRUCTURE OF THE E1BETA SUBUNIT OF PYRUVATE DEHYDROGENASE FROM THE ARCHEON PYROBACULUM AEROPHILUM
 
Authors :  G. Kleiger, J. Perry, D. Eisenberg
Date :  02 May 01  (Deposition) - 19 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  E1Beta, Pyruvate Dehydrogenase, Tetramer, Gxxxg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Kleiger, J. Perry, D. Eisenberg
3D Structure And Significance Of The Gphixxg Helix Packing Motif In Tetramers Of The E1Beta Subunit Of Pyruvate Dehydrogenase From The Archeon Pyrobaculum Aerophilum.
Biochemistry V. 40 14484 2001
PubMed-ID: 11724561  |  Reference-DOI: 10.1021/BI011016K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30EK/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: E1BETA SUBUNIT
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IK6)

(-) Sites  (0, 0)

(no "Site" information available for 1IK6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IK6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:183 -Pro A:184
2Asn A:241 -Pro A:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IK6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IK6)

(-) Exons   (0, 0)

(no "Exon" information available for 1IK6)

(-) Sequences/Alignments

Asymmetric 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:284
 aligned with Q8ZUR7_PYRAE | Q8ZUR7 from UniProtKB/TrEMBL  Length:320

    Alignment length:326
                                  1                                                                                                                                                                                                                                                                                                                               
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
         Q8ZUR7_PYRAE     - ------MANMAKAINMALHEEMERDERVVVLGEDVGKKGGVFLVTEGLYERFGPERVIDTPLNEGGILGFAMGMAMAGLKPVAEIQFVDFIWLGADELLNHIAKLRYRSGGNYKAPLVVRTPVGSGTRGGLYHSQSPEAIFVHTPGLVVVMPSTPYNAKGLLKAAIRGDDPVVFLEPKILYRAPREEVPEGDYVVEIGKARVAREGDDVTLVTYGAVVHKALEAAERVKASVEVVDLQTLNPLDFDTVLKSVSKTGRLIIAHDSPKTGGLGAEVAALVAEKALDRLTAPVIRLAGPDVPQSPIAHDAAYAPTVERIIKAIEYVMRY 320
               SCOP domains d1ik6a1 A:1-191 E1-beta subunit o         f pyruvate dehydrogenase, Pyr module                                                                                                                 d1ik6a2 A:192-326 E1-beta subunit of pyruvate dehydrogenase, C-domain                                                                   SCOP domains
               CATH domains ---1ik6A01 A:4-191  [code=3.40.50         .970, no name defined]                                                                                                                               1ik6A02 A:192-316  [code=3.40.50.920, no name defined]                                                                       ---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhh..eeeee.---------....hhhhhhh...eee...hhhhhhhhhhhhhhh..eeeee....----.hhhhhhhhhhhhhh------....eeeeee.-----------hhhhhhhh....eee...hhhhhhhhhhhhhhh...eeeeee.hhh....eeee...........eeee....eeeee..hhhhhhhhhhhh....eeeee..eee..hhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhhh....eeeee...------------.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ik6 A   1 VAGVVMMANMAKAINMALHEEMERDERVVVLGE---------LVTEGLYERFGPERVIDTPLNEGGILGFAMGMAMAGLKPVAEIQFV----LGADELLNHIAKLRY------KAPLVVRTPVG-----------SPEAIFVHTPGLVVVMPSTPYNAKGLLKAAIRGDDPVVFLEPKILYRAPREEVPEGDYVVEIGKARVAREGDDVTLVTYGAVVHKALEAAERVKASVEVVDLQTLNPLDFDTVLKSVSKTGRLIIAHDSPKTGGLGAEVRALVAEKALDRLTAPVIRLAGPDV------------PTVERIIKAIEYVMRY 326
                                    10        20        30  |      -  |     50        60        70        80       | -  |    100      |  -   |   120   |     -     | 140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       | -         -|      320      
                                                           33        43                                           88   93           107    114       124         136                                                                                                                                                               298          311
   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IK6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8ZUR7_PYRAE | Q8ZUR7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
biological process
    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.

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  Cis Peptide Bonds
    Ala A:183 - Pro A:184   [ RasMol ]  
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