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(-) Description

Title :  CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH SPERMINE
 
Authors :  W. Qiu, A. Dong, H. Ren, H. Wu, Y. Zhao, M. Schapira, G. Wasney, M. Vedadi, I. Kozieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundst A. N. Plotnikov, A. Bochkarev, R. Hui, Structural Genomics Consort
Date :  31 Oct 07  (Deposition) - 20 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transferase, Spermidine Synthase, Spermine, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Qiu, A. Dong, H. Ren, H. Wu, Y. Zhao, M. Schapira, G. Wasney, M. Vedadi J. Lew, I. Kozieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, A. N. Plotnikov, A. Bochkarev, R. Hui
Crystal Structure Of Spermidine Synthase From Plasmodium Falciparum In Complex With Spermine.
To Be Published
PubMed: search

(-) 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
    Fragment: RESIDUES 40-321
    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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MTA3Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
2SPM3Ligand/IonSPERMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MTA2Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
2SPM2Ligand/IonSPERMINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MTA2Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
2SPM2Ligand/IonSPERMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:51 , GLN A:93 , TYR A:102 , HIS A:103 , ASP A:127 , ASP A:196 , SER A:197 , ASP A:199 , GLN A:229 , GLU A:231 , TYR A:264 , PRO A:265 , ILE A:269 , MTA A:401 , HOH A:631BINDING SITE FOR RESIDUE SPM A 501
2AC2SOFTWARETRP B:51 , GLN B:93 , TYR B:102 , HIS B:103 , ASP B:127 , ASP B:196 , SER B:197 , ASP B:199 , GLN B:229 , GLU B:231 , TYR B:264 , MTA B:402 , HOH B:548BINDING SITE FOR RESIDUE SPM B 502
3AC3SOFTWARETRP C:51 , GLN C:93 , TYR C:102 , HIS C:103 , ASP C:127 , ASP C:196 , SER C:197 , ASP C:199 , GLU C:231 , SER C:232 , TYR C:264 , PRO C:265 , CYS C:268 , ILE C:269 , MTA C:403 , HOH C:611BINDING SITE FOR RESIDUE SPM C 503
4AC4SOFTWAREGLN A:72 , 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 , GLU A:177 , ASP A:178 , ALA A:179 , ASP A:196 , SER A:198 , PRO A:203 , ALA A:204 , THR A:206 , LEU A:207 , SPM A:501BINDING SITE FOR RESIDUE MTA A 401
5AC5SOFTWAREGLN 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 , SPM B:502BINDING SITE FOR RESIDUE MTA B 402
6AC6SOFTWAREGLN C:72 , LEU C:88 , GLN C:93 , GLY C:124 , ASP C:127 , CYS C:146 , GLU C:147 , ILE C:148 , ASP C:149 , VAL C:152 , ASP C:178 , ALA C:179 , ASP C:196 , SER C:198 , PRO C:203 , ALA C:204 , THR C:206 , SPM C:503BINDING SITE FOR RESIDUE MTA C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B7P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B7P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B7P)

(-) Exons   (0, 0)

(no "Exon" information available for 3B7P)

(-) 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 d3b7pa_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------3b7pA02 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...hhhhhh..eeeee.hhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b7p 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 d3b7pb_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------3b7pB02 B:98-320 Vaccinia Virus protein VP39                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b7p 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: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 d3b7pc_ C: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------3b7pC02 C:98-321 Vaccinia Virus protein VP39                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeeee.hhhhhhhhhhhh...hhhhhh..eeeee.hhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhh.....hhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b7p 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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B7P)

(-) 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 2pt9 2pwp 3rie 4bp1 4bp3 4cwa 4cxm 4uoe

(-) Related Entries Specified in the PDB File

2hte THE SAME PROTEIN IN COMPLEX WITH 5'-METHYLTHIOADENOSINE
2i7c THE SAME PROTEIN IN COMPLEX WITH AN INHIBITOR, ADODATO
2pwp THE SAME PROTEIN IN COMPLEX WITH SPERMIDINE