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(-) Description

Title :  CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE ALPHA CHAIN FROM AEROPYRUM PERNIX K1
 
Authors :  H. Niwa, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Prot Initiative (Rsgi)
Date :  06 Apr 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Coa-Binding Domain, Ligase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Niwa, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Succinyl-Coa Synthetase Alpha Chain From Aeropyrum Pernix K1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUCCINYL-COA SYNTHETASE ALPHA CHAIN
    ChainsA
    EC Number6.2.1.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSUCD
    Organism ScientificAEROPYRUM PERNIX
    Organism Taxid272557
    StrainK1

 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 2YV2)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:127 -Pro A:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:269
 aligned with Q9YD40_AERPE | Q9YD40 from UniProtKB/TrEMBL  Length:292

    Alignment length:287
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       
         Q9YD40_AERPE     4 LVDSETRVLVQGITGREGSFHAKAMLEYGTKVVAGVTPGKGGSEVHGVPVYDSVKEALAEHPEINTSIVFVPAPFAPDAVYEAVDAGIRLVVVITEGIPVHDTMRFVNYARQKGATIIGPNCPGAITPGQAKVGIMPGHIFKEGGVAVVSRSGTLTYEISYMLTRQGIGQSTVIGIGGDPIVGLSFTEALKLFQEDPQTEALVLIGEIGGDMEERAAEMIKKGEFTKPVIAYIAGRTAPPEKRMGHAGAIIMMGTGTYEGKVKALREAGVEVAETPFEVPELVRKAL 290
               SCOP domains d2yv2a1 A:9-128 Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain                                   d2yv2a2 A:129-295 Succinyl-CoA synthetase, alpha-chain, C-terminal domain                                                                                               SCOP domains
               CATH domains 2yv2A01 A:9-129 NAD(P)-binding Rossmann-like Domain                                                                      2yv2A02 A:130-295  [code=3.40.50.261, no name defined]                                                                                                                 CATH domains
               Pfam domains --CoA_binding-2yv2A01 A:11-105                                                                   ---------------------------------------------------Ligase_CoA-2yv2A02 A:157-279                                                                                               ---------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhhh.eeeeee.......ee..eeee.hhhhhhhhh....eeee..hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.eee.....eeee...eeee..hhhhh....eeeee.hhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhh.....eeeeee....hhhhhhhhhhhh......eeeee...------------------..hhhhhhhhhhh...eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv2 A   9 LVDSETRVLVQGITGREGSFHAKAMLEYGTKVVAGVTPGKGGSEVHGVPVYDSVKEALAEHPEINTSIVFVPAPFAPDAVYEAVDAGIRLVVVITEGIPVHDTMRFVNYARQKGATIIGPNCPGAITPGQAKVGIMPGHIFKEGGVAVVSRSGTLTYEISYMLTRQGIGQSTVIGIGGDPIVGLSFTEALKLFQEDPQTEALVLIGEIGGDMEERAAEMIKKGEFTKPVIAYIAGR------------------TGTYEGKVKALREAGVEVAETPFEVPELVRKAL 295
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238     |   -         -    |  268       278       288       
                                                                                                                                                                                                                                                                     244                263                                

   Legend:   → Mismatch (orange background)
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  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/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9YD40_AERPE | Q9YD40)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004775    succinate-CoA ligase (ADP-forming) activity    Catalysis of the reaction: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate.
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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    Gly A:127 - Pro A:128   [ RasMol ]  
 

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