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(-) Description

Title :  THE STRUCTURE OF PLASMODIUM FALCIPARUM SPERMIDINE SYNTHASE IN COMPLEX WITH DECARBOXYLATED S-ADENOSYLMETHIONINE AND THE INHIBITOR CIS-4-METHYLCYCLOHEXYLAMINE (4MCHA)
 
Authors :  V. T. Dufe, W. Qiu, I. B. Muller, R. Hui, R. D. Walter, S. Al-Karadaghi, St Genomics Consortium (Sgc)
Date :  08 May 07  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transferase, Spermidine Synthase, Structural Genomics Consortium, Sgc, Inhibitor Complex, Structural Biology Of Malarial Parasites And Other Apicomplexans (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. T. Dufe, W. Qiu, I. B. Muller, R. Hui, R. D. Walter, S. Al-Karadaghi
Crystal Structure Of Plasmodium Falciparum Spermidine Synthase In Complex With The Substrate Decarboxylated S-Adenosylmethionine And The Potent Inhibitors 4Mcha And Adodato.
J. Mol. Biol. V. 373 167 2007
PubMed-ID: 17822713  |  Reference-DOI: 10.1016/J.JMB.2007.07.053

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B, C
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC
    Expression System Strain: BL21-(DE3)-ROSETTA OXFORD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
11PG2Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
22MH3Ligand/IonCIS-4-METHYLCYCLOHEXANAMINE
3GOL3Ligand/IonGLYCEROL
4S4M3Ligand/Ion5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
11PG2Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
22MH2Ligand/IonCIS-4-METHYLCYCLOHEXANAMINE
3GOL2Ligand/IonGLYCEROL
4S4M2Ligand/Ion5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE
5SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (5, 8)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
22MH2Ligand/IonCIS-4-METHYLCYCLOHEXANAMINE
3GOL2Ligand/IonGLYCEROL
4S4M2Ligand/Ion5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE
5SO41Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:236 , GLY B:238 , THR B:239 , LYS B:291BINDING SITE FOR RESIDUE SO4 B 604
02AC2SOFTWAREGLN A:72 , GLN A:93 , HIS A:103 , GLY A:124 , GLY A:125 , ASP A:127 , CYS A:146 , GLU A:147 , ILE A:148 , ASP A:178 , ALA A:179 , ASP A:196 , SER A:198 , PRO A:203 , ALA A:204 , THR A:206 , LEU A:207BINDING SITE FOR RESIDUE S4M A 501
03AC3SOFTWAREGLN B:72 , LEU B:88 , GLN B:93 , TYR B:102 , HIS B:103 , GLY B:124 , GLY B:125 , ASP B:127 , CYS B:146 , GLU B:147 , ILE B:148 , ASP B:178 , ALA B:179 , ASP B:196 , SER B:198 , PRO B:203 , ALA B:204 , THR B:206 , LEU B:207 , HOH B:614BINDING SITE FOR RESIDUE S4M B 502
04AC4SOFTWAREGLN C:71 , GLN C:92 , TYR C:101 , HIS C:102 , GLY C:123 , ASP C:126 , CYS C:145 , GLU C:146 , ILE C:147 , GLU C:176 , ASP C:177 , ALA C:178 , ASP C:195 , SER C:197 , PRO C:202 , ALA C:203 , LEU C:206 , TYR C:263BINDING SITE FOR RESIDUE S4M C 503
05AC5SOFTWAREGLN A:93 , ASP A:199 , TYR A:264 , HOH A:724BINDING SITE FOR RESIDUE 2MH A 401
06AC6SOFTWAREILE B:92 , GLN B:93 , TYR B:102 , SER B:197 , ASP B:199 , TYR B:264 , ILE B:269 , HOH B:606BINDING SITE FOR RESIDUE 2MH B 402
07AC7SOFTWARETRP C:50 , ILE C:91 , GLN C:92 , SER C:196 , ASP C:198 , TYR C:263 , PRO C:264 , ILE C:268 , HOH C:755BINDING SITE FOR RESIDUE 2MH C 403
08AC8SOFTWARETRP A:43 , SER A:45 , PHE A:47 , SER A:57BINDING SITE FOR RESIDUE 1PG A 701
09AC9SOFTWARELYS B:42 , PHE B:47 , SER B:57 , SER C:44 , PHE C:46 , SER C:56BINDING SITE FOR RESIDUE 1PG C 702
10BC1SOFTWARELYS B:97 , HOH B:651 , TRP C:233BINDING SITE FOR RESIDUE GOL B 601
11BC2SOFTWARETRP B:234 , LYS C:96 , PHE C:99 , HOH C:772BINDING SITE FOR RESIDUE GOL C 602
12BC3SOFTWARELYS A:97 , PHE A:100 , TRP A:234BINDING SITE FOR RESIDUE GOL A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PT9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PT9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PT9)

(-) Exons   (0, 0)

(no "Exon" information available for 2PT9)

(-) 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 d2pt9a_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------2pt9A02 A:98-321 Vaccinia Virus protein VP39                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........eeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhh..hhhhhhh..eeeee.hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pt9 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:280
 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 d2pt9b_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------2pt9B02 B:98-320 Vaccinia Virus protein VP39                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pt9 B  41 KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIEN 320
                                    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 C from PDB  Type:PROTEIN  Length:280
 aligned with Q8II73_PLAF7 | Q8II73 from UniProtKB/TrEMBL  Length:321

    Alignment length:280
                                    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
         Q8II73_PLAF7    42 KWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIENI 321
               SCOP domains d2pt9c_ C: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------2pt9C02 C:97-320 Vaccinia Virus protein VP39                                                                                                                                                                                     CATH domains
           Pfam domains (1) Spermine_synth-2pt9C01 C:41-283                                                                                                                                                                                                                    ------------------------------------- Pfam domains (1)
           Pfam domains (2) Spermine_synth-2pt9C02 C:41-283                                                                                                                                                                                                                    ------------------------------------- Pfam domains (2)
           Pfam domains (3) Spermine_synth-2pt9C03 C:41-283                                                                                                                                                                                                                    ------------------------------------- Pfam domains (3)
         Sec.struct. author .eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pt9 C  41 KWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDGVIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSVENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTYDVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTIKNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLESKEFADLKYYNYENHSAAFKLPAFLLKEIENI 320
                                    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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  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  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) 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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8II73_PLAF7 | Q8II73: 2hte 2i7c 2pss 2pt6 2pwp 3b7p 3rie 4bp1 4bp3 4cwa 4cxm 4uoe

(-) Related Entries Specified in the PDB File

2hte THE CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM P. FALCIPARUM IN COMPLEX WITH MTA
2i7c THE CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM P. FALCIPARUM IN COMPLEX WITH ADODATO
2pss THE CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM P. FALCIPARUM IN ITS APO FORM.
2pt6 THE CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM P. FALCIPARUM IN COMPLEX WITH DCADOMET