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(-) Description

Title :  STRUCTURE OF PLASMODIUM FALCIPARUM SPERMIDINE SYNTHASE IN COMPLEX WITH 1H-BENZIMIDAZOLE-2-PENTANAMINE
 
Authors :  J. Sprenger, J. C. Halander, B. Svensson, S. Al-Karadaghi, L. Persson
Date :  01 Apr 14  (Deposition) - 08 Oct 14  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transferase, Aminopropyl Transferase, Polyamine Pathway, Rossmann-Like Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sprenger, B. Svensson, J. Halander, J. Carey, L. Persson, S. Al-Karadaghi
Three-Dimensional Structures Of Plasmodium Falciparum Spermidine Synthase With Bound Inhibitors Suggest New Strategies For Drug Design.
Acta Crystallogr. , Sect. D V. 71 484 2015
PubMed-ID: 25760598  |  Reference-DOI: 10.1107/S1399004714027011

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B, C
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-TEV-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 40-321
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2JA22Ligand/Ion5-(1H-BENZIMIDAZOL-2-YL)PENTAN-1-AMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11PG-1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2JA22Ligand/Ion5-(1H-BENZIMIDAZOL-2-YL)PENTAN-1-AMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2JA21Ligand/Ion5-(1H-BENZIMIDAZOL-2-YL)PENTAN-1-AMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:51 , GLN A:93 , TYR A:102 , GLY A:125 , GLY A:126 , ASP A:127 , GLU A:147 , ASP A:196 , SER A:197 , SER A:198 , ASP A:199 , TYR A:264 , PRO A:265BINDING SITE FOR RESIDUE JA2 A 601
2AC2SOFTWARESER B:45 , SER B:57 , TRP C:43 , SER C:45 , PHE C:47BINDING SITE FOR RESIDUE 1PG B 601
3AC3SOFTWARETRP C:51 , GLN C:93 , TYR C:102 , GLY C:126 , ASP C:127 , ASP C:196 , SER C:197 , SER C:198 , ASP C:199 , TYR C:264 , PRO C:265 , HOH C:2005 , HOH C:2094BINDING SITE FOR RESIDUE JA2 C 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CWA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CWA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CWA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CWA)

(-) Exons   (0, 0)

(no "Exon" information available for 4CWA)

(-) Sequences/Alignments

Asymmetric 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:281
 aligned with Q8II73_PLAF7 | Q8II73 from UniProtKB/TrEMBL  Length:321

    Alignment length:281
                                    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 
         Q8II73_PLAF7    41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIENI 321
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........eeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeee..hhhhhhhhhhhh...hhhhhh..eeee..hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cwa A  41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIENI 321
                                    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 


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with Q8II73_PLAF7 | Q8II73 from UniProtKB/TrEMBL  Length:321

    Alignment length:280
                                    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
         Q8II73_PLAF7    41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIEN 320
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhh....eeeeeee.-------------hhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cwa B  41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDS-------------NFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIEN 320
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      |  -         -|      220       230       240       250       260       270       280       290       300       310       320
                                                                                                                                                                                      197           211                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with Q8II73_PLAF7 | Q8II73 from UniProtKB/TrEMBL  Length:321

    Alignment length:281
                                    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 
         Q8II73_PLAF7    41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIENI 321
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cwa C  41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIENI 321
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 4CWA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CWA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CWA)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8II73_PLAF7 | Q8II73)
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:0006596    polyamine biosynthetic process    The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
    GO:0008295    spermidine biosynthetic process    The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
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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 Related Entries

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        Q8II73_PLAF7 | Q8II73: 2hte 2i7c 2pss 2pt6 2pt9 2pwp 3b7p 3rie 4bp1 4bp3 4cxm 4uoe

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