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(-) Description

Title :  THE STRUCTURE OF PLASMODIUM FALCIPARUM SPERMIDINE SYNTHASE IN COMPLEX WITH 5'-METHYLTHIOADENOSINE AND N-(3-AMINOPROPYL)-TRANS-CYCLOHEXANE-1,4-DIAMINE
 
Authors :  M. Williams, J. Sprenger, L. Persson, A. I. Louw, L. Birkholtz, S. Al-Ka
Date :  13 Apr 11  (Deposition) - 25 Apr 12  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Rossmann-Like Fold, Rossmann Fold, Spermidine Synthesis, Aminopropyl Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. B. Burger, M. Williams, J. Sprenger, S. B. Reeksting, M. Botha, I. B. Muller, F. Joubert, L. M. Birkholtz, A. I. Louw
A Novel Inhibitor Of Plasmodium Falciparum Spermidine Synthase: A Twist In The Tail.
Malar J V. 14 54 2015
PubMed-ID: 25651815  |  Reference-DOI: 10.1186/S12936-015-0572-Z

(-) 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: UNP RESIDUES 41-321
    Gene: PF11_0301
    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  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2GOL3Ligand/IonGLYCEROL
3JFQ3Ligand/IonTRANS-N-(3-AMINOPROPYL)CYCLOHEXANE-1,4-DIAMINE
4MTA3Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
11PG-1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2GOL2Ligand/IonGLYCEROL
3JFQ2Ligand/IonTRANS-N-(3-AMINOPROPYL)CYCLOHEXANE-1,4-DIAMINE
4MTA2Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2GOL2Ligand/IonGLYCEROL
3JFQ2Ligand/IonTRANS-N-(3-AMINOPROPYL)CYCLOHEXANE-1,4-DIAMINE
4MTA2Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:72 , LEU A:88 , GLN A:93 , GLY A:124 , GLY A:125 , ASP A:127 , CYS A:146 , GLU A:147 , ILE A:148 , ASP A:149 , VAL A:152 , ASP A:178 , ALA A:179 , ASP A:196 , SER A:198 , PRO A:203 , ALA A:204 , THR A:206 , JFQ A:501BINDING SITE FOR RESIDUE MTA A 401
02AC2SOFTWAREILE A:92 , GLN A:93 , TYR A:102 , HIS A:103 , ASP A:127 , ASP A:196 , SER A:197 , ASP A:199 , TYR A:264 , ILE A:269 , MTA A:401 , HOH A:831BINDING SITE FOR RESIDUE JFQ A 501
03AC3SOFTWARELYS A:97 , TRP A:234 , HOH A:835 , HOH A:858 , HOH A:927BINDING SITE FOR RESIDUE GOL A 601
04AC4SOFTWAREGLN B:72 , LEU B:88 , GLN B:93 , GLY B:124 , GLY B:125 , ASP B:127 , CYS B:146 , GLU B:147 , ILE B:148 , ASP B:149 , VAL B:152 , ASP B:178 , ALA B:179 , ASP B:196 , SER B:197 , SER B:198 , PRO B:203 , ALA B:204 , THR B:206 , LEU B:207 , JFQ B:501BINDING SITE FOR RESIDUE MTA B 401
05AC5SOFTWAREILE B:92 , GLN B:93 , TYR B:102 , HIS B:103 , ASP B:127 , ASP B:196 , SER B:197 , ASP B:199 , TYR B:264 , ILE B:269 , MTA B:401 , HOH B:802 , HOH B:981BINDING SITE FOR RESIDUE JFQ B 501
06AC6SOFTWARELYS B:97 , LYS B:297 , HOH B:946 , HOH B:989 , HOH B:990 , TRP C:234BINDING SITE FOR RESIDUE GOL B 602
07AC7SOFTWARETRP C:43 , SER C:45 , PHE C:47 , HOH C:989BINDING SITE FOR RESIDUE 1PG C 701
08AC8SOFTWAREGLN C:72 , LEU C:88 , GLN C:93 , GLY C:124 , GLY C:125 , ASP C:127 , CYS C:146 , GLU C:147 , ILE C:148 , VAL C:152 , ASP C:178 , ALA C:179 , ASP C:196 , SER C:198 , PRO C:203 , ALA C:204 , THR C:206 , LEU C:207 , JFQ C:501BINDING SITE FOR RESIDUE MTA C 401
09AC9SOFTWAREILE C:92 , GLN C:93 , TYR C:102 , HIS C:103 , ASP C:127 , ASP C:196 , SER C:197 , ASP C:199 , TYR C:264 , ILE C:269 , MTA C:401 , HOH C:805 , HOH C:875BINDING SITE FOR RESIDUE JFQ C 501
10BC1SOFTWARETRP B:234 , LYS C:97 , HOH C:832 , HOH C:865 , HOH C:958 , HOH C:1010 , HOH C:1015BINDING SITE FOR RESIDUE GOL C 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RIE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RIE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RIE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RIE)

(-) Exons   (0, 0)

(no "Exon" information available for 3RIE)

(-) 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 d3riea_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........eeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeeee.hhhhhhhhhhhh...hhhhhh..eeeee.hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rie 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:279
 aligned with Q8II73_PLAF7 | Q8II73 from UniProtKB/TrEMBL  Length:321

    Alignment length:279
                                    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         
         Q8II73_PLAF7    41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIE 319
               SCOP domains d3rieb_ B: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rie B  41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIE 319
                                    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         


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 d3riec_ C: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhh...hhhhhh..eeeee.hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rie 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)
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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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RIE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RIE)

(-) 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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        Q8II73_PLAF7 | Q8II73: 2hte 2i7c 2pss 2pt6 2pt9 2pwp 3b7p 4bp1 4bp3 4cwa 4cxm 4uoe

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