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(-) Description

Title :  CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE ALPHA CHAIN FROM METHANOCALDOCOCCUS JANNASCHII DSM 2661
 
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 :  1.70
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 Methanocaldococcus Jannaschii Dsm 2661
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUCCINYL-COA LIGASE [ADP-FORMING] SUBUNIT ALPHA
    ChainsA
    EC Number6.2.1.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSUCD
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid243232
    StrainDSM 2661
    SynonymSUCCINYL-COA SYNTHETASE SUBUNIT ALPHA, SCS-ALPHA

 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 2YV1)

(-) Sites  (0, 0)

(no "Site" information available for 2YV1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YV1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:126 -Pro A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YV1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUCCINYL_COA_LIG_1PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.SUCD_METJA157-186  1A:157-186
2SUCCINYL_COA_LIG_2PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.SUCD_METJA240-253  1A:240-241

(-) Exons   (0, 0)

(no "Exon" information available for 2YV1)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:268
 aligned with SUCD_METJA | Q58643 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:287
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       
           SUCD_METJA     7 MILLDENTKAIVQGITGRQGSFHTKKMLECGTKIVGGVTPGKGGQNVHGVPVFDTVKEAVKETDANASVIFVPAPFAKDAVFEAIDAGIELIVVITEHIPVHDTMEFVNYAEDVGVKIIGPNTPGIASPKVGKLGIIPMEVLKEGSVGMVSRSGTLTYEIAHQIKKAGFGVSTCVGIGGDPIVGLRYKEVLDLFEKDDETEAIVMIGEIGGGAEEEAAKFIEKMKKPVIGYIAGQSAPEGKRMGHAGAIVEKGKGTAESKMKALEEAGAYVAKNISDIPKLLAGILG 293
               SCOP domains d2yv1a1 A:7-127 Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain                                    d2yv1a2 A:128-293 Succinyl-CoA synthetase, alpha-chain, C-terminal domain                                                                                              SCOP domains
               CATH domains 2yv1A01 A:7-128 NAD(P)-binding Rossmann-like Domain                                                                       2yv1A02 A:129-292  [code=3.40.50.261, no name defined]                                                                                                              - CATH domains
               Pfam domains ----CoA_binding-2yv1A01 A:11-104                                                                  ---------------------------------------------------Ligase_CoA-2yv1A02 A:156-276                                                                                             ----------------- Pfam domains
         Sec.struct. author .........eeee...hhhhhhhhhhhhhh...eeeee.......ee..eeee.hhhhhhhhhh..eeee..hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.eee.....eeee...eeee..hhhhh....eeeee..hhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhh.....eeeeeee...hhhhhhhhhhh.....eeeeee..-------------------.hhhhhhhhhhhhh.ee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_1            -----------------------------------------------------SUCCINYL_COA_L---------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv1 A   7 MILLDENTKAIVQGITGRQGSFHTKKMLECGTKIVGGVTPGKGGQNVHGVPVFDTVKEAVKETDANASVIFVPAPFAKDAVFEAIDAGIELIVVITEHIPVHDTMEFVNYAEDVGVKIIGPNTPGIASPKVGKLGIIPMEVLKEGSVGMVSRSGTLTYEIAHQIKKAGFGVSTCVGIGGDPIVGLRYKEVLDLFEKDDETEAIVMIGEIGGGAEEEAAKFIEKMKKPVIGYIAGQ-------------------GTAESKMKALEEAGAYVAKNISDIPKLLAGILG 293
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    |    -         -    |  266       276       286       
                                                                                                                                                                                                                                                                    241                 261                                

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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/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUCD_METJA | Q58643)
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.
    GO:0009142    nucleoside triphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0006105    succinate metabolic process    The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle.
    GO:0006104    succinyl-CoA metabolic process    The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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    Gly A:126 - Pro A:127   [ RasMol ]  
 

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