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(-) Description

Title :  CLONING, EXPRESSION, CHARACTERISATION AND THREE-DIMENSIONAL STRUCTURE DETERMINATION OF THE CAENORHABDITIS ELEGANS SPERMIDINE SYNTHASE
 
Authors :  V. T. Dufe, K. Luersen, M. L. Eschbach, N. Haider, T. Karlberg, R. D. Walter, S. Al-Karadaghi
Date :  19 Sep 05  (Deposition) - 15 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. T. Dufe, K. Luersen, M. L. Eschbach, N. Haider, T. Karlberg, R. D. Walter, S. Al-Karadaghi
Cloning, Expression, Characterisation And Three-Dimensional Structure Determination Of Caenorhabditis Elegans Spermidine Synthase
Febs Lett. V. 579 6037 2005
PubMed-ID: 16226262  |  Reference-DOI: 10.1016/J.FEBSLET.2005.09.050
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    ChainsA, B
    EC Number2.5.1.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRCHISB
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2B2C)

(-) Sites  (0, 0)

(no "Site" information available for 2B2C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B2C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B2C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B2C)

(-) Exons   (0, 0)

(no "Exon" information available for 2B2C)

(-) 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:276
 aligned with G5EFG3_CAEEL | G5EFG3 from UniProtKB/TrEMBL  Length:314

    Alignment length:312
                                    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  
         G5EFG3_CAEEL     3 KLHKGWFTEFSPDDLEKMNGASDEEPTKVLKSDGQEMGGAWPGQAFSLQVKKVLFHEKSKYQDVLVFESTTYGNVLVLDGIVQATERDEFSYQEMLAHLPMFAHPDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKKFLPGMSCGFSHPKLDLFCGDGFEFLKNHKNEFDVIITDSSDPVGPAESLFGQSYYELLRDALKEDGILSSQGESVWLHLPLIAHLVAFNRKIFPAVTYAQSIVSTYPSGSMGYLICAKNANRDVTTPARTLTAEQIKALNLRFYNSEVHKAAFVLPQFVKNALE 314
               SCOP domains d2b2ca1 A:3-314                        Spermidine synthase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------                       -------------------------------------------------2b2cA02 A:90-314 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee.....-----------------------.....eeeeeeeeeeeeeee....eeeeeee...eeeeee..eeeee....hhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeee..hhhhhhhhhhhh...hhhhhh..eeee..hhhhhhhhh...eeeeee..-------------hhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee...hhh.eeeeeeee..............hhhhhhhh.....hhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b2c A   3 KLHKGWFTEFSPDDL-----------------------GAWPGQAFSLQVKKVLFHEKSKYQDVLVFESTTYGNVLVLDGIVQATERDEFSYQEMLAHLPMFAHPDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKKFLPGMSCGFSHPKLDLFCGDGFEFLKNHKNEFDVIITDS-------------SYYELLRDALKEDGILSSQGESVWLHLPLIAHLVAFNRKIFPAVTYAQSIVSTYPSGSMGYLICAKNANRDVTTPARTLTAEQIKALNLRFYNSEVHKAAFVLPQFVKNALE 314
                                    12    |    -         -        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      |  -         -|      212       222       232       242       252       262       272       282       292       302       312  
                                         17                      41                                                                                                                                                 189           203                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with G5EFG3_CAEEL | G5EFG3 from UniProtKB/TrEMBL  Length:314

    Alignment length:312
                                    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  
         G5EFG3_CAEEL     3 KLHKGWFTEFSPDDLEKMNGASDEEPTKVLKSDGQEMGGAWPGQAFSLQVKKVLFHEKSKYQDVLVFESTTYGNVLVLDGIVQATERDEFSYQEMLAHLPMFAHPDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKKFLPGMSCGFSHPKLDLFCGDGFEFLKNHKNEFDVIITDSSDPVGPAESLFGQSYYELLRDALKEDGILSSQGESVWLHLPLIAHLVAFNRKIFPAVTYAQSIVSTYPSGSMGYLICAKNANRDVTTPARTLTAEQIKALNLRFYNSEVHKAAFVLPQFVKNALE 314
               SCOP domains d2b2cb_ B: auto                       mated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------                       -------------------------------------------------2b2cB02 B:90-314 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee.....-----------------------.....eeeeeeeeeeeeeee....eeeeeee...eeeeee..eeeee....hhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeee..hhhhhhhhhhhh...hhhhhh..eeee..hhhhhhhhh...eeeeee..-------------hhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee...hhh.eeeeeeee..............hhhhhhhh.....hhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b2c B   3 KLHKGWFTEFSPDDL-----------------------GAWPGQAFSLQVKKVLFHEKSKYQDVLVFESTTYGNVLVLDGIVQATERDEFSYQEMLAHLPMFAHPDPKRVLIIGGGDGGILREVLKHESVEKVTMCEIDEMVIDVAKKFLPGMSCGFSHPKLDLFCGDGFEFLKNHKNEFDVIITDS-------------SYYELLRDALKEDGILSSQGESVWLHLPLIAHLVAFNRKIFPAVTYAQSIVSTYPSGSMGYLICAKNANRDVTTPARTLTAEQIKALNLRFYNSEVHKAAFVLPQFVKNALE 314
                                    12    |    -         -        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      |  -         -|      212       222       232       242       252       262       272       282       292       302       312  
                                         17                      41                                                                                                                                                 189           203                                                                                                               

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B2C)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G5EFG3_CAEEL | G5EFG3)
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.
    GO:0004766    spermidine synthase activity    Catalysis of the reaction: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine.
    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.
biological process
    GO:0006595    polyamine metabolic process    The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.

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