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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ISOZYME OF CITRATE SYNTHASE FROM SULFOLBUS TOKODAII STRAIN7
 
Authors :  M. Murakami, K. Ihara, T. Kouyama
Date :  27 Apr 04  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Open Form, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Murakami, K. Ihara, T. Kouyama
Crystal Structures Of Two Isozymes Of Citrate Synthase From Sulfolbus Tokodaii Strain7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 378AA LONG HYPOTHETICAL CITRATE SYNTHASE
    Chains: A, B
    EC Number: 2.3.3.1, 4.1.3.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: STRAIN7
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 111955

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:219 , GOL A:401 , HOH A:589 , HOH A:797 , HOH A:800BINDING SITE FOR RESIDUE SO4 A 411
2AC2SOFTWAREHIS A:219 , GLY A:220 , GLY A:221 , ALA A:222 , ALA A:223 , GLU A:224 , THR A:332 , PHE A:335 , SO4 A:411 , HOH A:528BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VGM)

(-) 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:376
 aligned with Q96ZM7_SULTO | Q96ZM7 from UniProtKB/TrEMBL  Length:378

    Alignment length:376
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372      
         Q96ZM7_SULTO     3 VEVSRGLENVIIKTTGLTYIDGINGILRYRGYDINDLVNYASYEELIHLMLYGELPNRQQLNQIKGIINESFEVPEQVISTIFSMPRNCDAIGMMETAFGILASIYDPKWNRATNKELAVQIIAKTATITANIYRAKEGLKPKIPEPSESYAESFLAATFGKKPTQEEIKAMDASLILYTDHEVPASTTAALVASSTLSDMYSCIVAALAALKGPLHGGAAEEAFKQFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDPRAKIFKTLAKSFAEKNENVKKYYEIAERIEKLGVDTFGSKHIYPNTDFYSGIVFYALGFPIYMFTSLFALSRVLGWLAHIIEYVEEQHRLIRPRALYIGPEKREFKPIELR 378
               SCOP domains d1vgma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------1vgmA01 A:15-220,A:325-358 Citrate Synthase, domain 1                                                                                                                                                         1vgmA02 A:221-324 Cytochrome P450-Terp, domain 2                                                        1vgmA01 A:15-220,A:325-358        -------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeeee..eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgm A   3 VEVSRGLENVIIKTTGLTYIDGINGILRYRGYDINDLVNYASYEELIHLMLYGELPNRQQLNQIKGIINESFEVPEQVISTIFSMPRNCDAIGMMETAFGILASIYDPKWNRATNKELAVQIIAKTATITANIYRAKEGLKPKIPEPSESYAESFLAATFGKKPTQEEIKAMDASLILYTDHEVPASTTAALVASSTLSDMYSCIVAALAALKGPLHGGAAEEAFKQFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDPRAKIFKTLAKSFAEKNENVKKYYEIAERIEKLGVDTFGSKHIYPNTDFYSGIVFYALGFPIYMFTSLFALSRVLGWLAHIIEYVEEQHRLIRPRALYIGPEKREFKPIELR 378
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372      


Chain B from PDB  Type:PROTEIN  Length:376
 aligned with Q96ZM7_SULTO | Q96ZM7 from UniProtKB/TrEMBL  Length:378

    Alignment length:376
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372      
         Q96ZM7_SULTO     3 VEVSRGLENVIIKTTGLTYIDGINGILRYRGYDINDLVNYASYEELIHLMLYGELPNRQQLNQIKGIINESFEVPEQVISTIFSMPRNCDAIGMMETAFGILASIYDPKWNRATNKELAVQIIAKTATITANIYRAKEGLKPKIPEPSESYAESFLAATFGKKPTQEEIKAMDASLILYTDHEVPASTTAALVASSTLSDMYSCIVAALAALKGPLHGGAAEEAFKQFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDPRAKIFKTLAKSFAEKNENVKKYYEIAERIEKLGVDTFGSKHIYPNTDFYSGIVFYALGFPIYMFTSLFALSRVLGWLAHIIEYVEEQHRLIRPRALYIGPEKREFKPIELR 378
               SCOP domains d1vgmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------1vgmB01 B:15-220,B:325-358 Citrate Synthase, domain 1                                                                                                                                                         1vgmB02 B:221-324 Cytochrome P450-Terp, domain 2                                                        1vgmB01 B:15-220,B:325-358        -------------------- CATH domains
           Pfam domains (1) -----Citrate_synt-1vgmB01 B:8-360                                                                                                                                                                                                                                                                                                                                     ------------------ Pfam domains (1)
           Pfam domains (2) -----Citrate_synt-1vgmB02 B:8-360                                                                                                                                                                                                                                                                                                                                     ------------------ Pfam domains (2)
         Sec.struct. author ...hhhhh..eeeee..eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgm B   3 VEVSRGLENVIIKTTGLTYIDGINGILRYRGYDINDLVNYASYEELIHLMLYGELPNRQQLNQIKGIINESFEVPEQVISTIFSMPRNCDAIGMMETAFGILASIYDPKWNRATNKELAVQIIAKTATITANIYRAKEGLKPKIPEPSESYAESFLAATFGKKPTQEEIKAMDASLILYTDHEVPASTTAALVASSTLSDMYSCIVAALAALKGPLHGGAAEEAFKQFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDPRAKIFKTLAKSFAEKNENVKKYYEIAERIEKLGVDTFGSKHIYPNTDFYSGIVFYALGFPIYMFTSLFALSRVLGWLAHIIEYVEEQHRLIRPRALYIGPEKREFKPIELR 378
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Citrate_synt] (9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q96ZM7_SULTO | Q96ZM7)
molecular function
    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).
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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