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(-) Description

Title :  CRYSTAL STRUCTURE OF PIG GTP-SPECIFIC SUCCINYL-COA SYNTHETASE FROM POLYETHYLENE GLYCOL
 
Authors :  M. E. Fraser
Date :  16 Jan 06  (Deposition) - 21 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Active Site Phosphohistidine Residue, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Fraser, K. Hayakawa, M. S. Hume, D. G. Ryan, E. R. Brownie
Interactions Of Gtp With The Atp-Grasp Domain Of Gtp-Specific Succinyl-Coa Synthetase
J. Biol. Chem. V. 281 11058 2006
PubMed-ID: 16481318  |  Reference-DOI: 10.1074/JBC.M511785200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCCINYL-COA LIGASE [GDP-FORMING] ALPHA-CHAIN, MITOCHONDRIAL
    ChainsA
    EC Number6.2.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSUCLG1
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymSUCCINYL-COA SYNTHETASE, ALPHA CHAIN, SCS-ALPHA
 
Molecule 2 - SUCCINYL-COA LIGASE [GDP-FORMING] BETA-CHAIN, MITOCHONDRIAL
    ChainsB
    EC Number6.2.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSUCLG2
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymSUCCINYL-COA SYNTHETASE, BETAG CHAIN, SCS-BETAG, GTP- SPECIFIC SUCCINYL-COA SYNTHETASE BETA SUBUNIT, FRAGMENT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:255 , ARG A:256 , ASP B:227 , LYS B:258BINDING SITE FOR RESIDUE SO4 A 307
2AC2SOFTWAREGLY B:52 , GLY B:53 , ARG B:54 , LYS B:222BINDING SITE FOR RESIDUE SO4 B 396

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:129 -Pro A:130
2Asn B:206 -Pro B:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUCCINYL_COA_LIG_1PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.SUCA_PIG200-229  1A:160-189
2SUCCINYL_COA_LIG_2PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.SUCA_PIG288-301  1A:248-261
3SUCCINYL_COA_LIG_3PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3.SUCB2_PIG302-327  1B:264-289

(-) Exons   (0, 0)

(no "Exon" information available for 2FPI)

(-) 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:305
 aligned with SUCA_PIG | O19069 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:305
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341     
             SUCA_PIG    42 SYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMVRVKHRLLRQGKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKML 346
               SCOP domains d2fpia1 A:2-130 Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain                                            d2fpia2 A:131-306 Succinyl-CoA synthetase, alpha-chain, C-terminal domain                                                                                                        SCOP domains
               CATH domains -------2fpiA01 A:9-131 NAD(P)-binding Rossmann-like Domain                                                                        2fpiA02 A:132-301  [code=3.40.50.261, no name defined]                                                                                                                    ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh.eeee..................hhhhhhhhhh..eeee.....hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.....eee.....eeee...eeee..hhhhh.eeeeeeee..hhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhh.......eeeeee......................hhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_1            ----------------------------------------------------------SUCCINYL_COA_L--------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fpi A   2 SYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMVRVKHRLLRQGKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKSKPVVSFIAGLTAPPGRRMGhAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKML 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
                                                                                                                                                                                                                                                                                           259-NEP                                           

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with SUCB2_PIG | P53590 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:393
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428   
            SUCB2_PIG    39 LNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQILAGGRGKGVFSSGLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKESQVYQAFKLLTADPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT 431
               SCOP domains d2fpib2 B:1-245 Succinyl-CoA synthetase, beta-chain, N-terminal domain                                                                                                                                                                               d2fpib1 B:246-393 Succinyl-CoA synthetase, beta-chain, C-terminal domain                                                                             SCOP domains
               CATH domains 2fpiB01             2fpiB02 B:21-111 ATP-grasp fold, A domain                                                  2fpiB01 B:1-20,B:112-246 ATP-grasp fold, B domain                                                                                      2fpiB03 B:247-392  [code=3.40.50.261, no name defined]                                                                                            - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh......eeee.hhhhhhhhhhhhh...eeeee..........ee.......eee..hhhhhhhhhhh....eee........ee...eeeee.....eeeeeeeee......eeeeee........hhhhhhhhhheeee.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.....eee..eeeee.hhhhhhhhhhhhh......hhhhhhhhhh..eeee....eeeee.hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhh.........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_3        -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fpi B   1 MNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQILAGGRGKGVFSSGLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKESQVYQAFKLLTADPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT 393
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390   

   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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FPI)

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUCA_PIG | O19069)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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.
    GO:0004776    succinate-CoA ligase (GDP-forming) activity    Catalysis of the reaction: GTP + succinate + CoA = GDP + 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.
    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: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.

Chain B   (SUCB2_PIG | P53590)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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: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:0004776    succinate-CoA ligase (GDP-forming) activity    Catalysis of the reaction: GTP + succinate + CoA = GDP + 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: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: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
        SUCA_PIG | O190691euc 1eud 2fp4 2fpg 2fpp 4xx0 5cae
        SUCB2_PIG | P535901euc 1eud 2fp4 2fpg 2fpp 4xx0 5cae

(-) Related Entries Specified in the PDB File

1euc 1eud 2fp4 2fpg 2fpp