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(-) Description

Title :  HUMAN SPERMIDINE SYNTHASE
 
Authors :  J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  27 Nov 06  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Spermidine Synthase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, J. Min, Y. Ikeguchi, H. Zeng, A. Dong, P. Loppnau, A. E. Pegg, A. N. Plotnikov
Structure And Mechanism Of Spermidine Synthases.
Biochemistry V. 46 8331 2007
PubMed-ID: 17585781  |  Reference-DOI: 10.1021/BI602498K
(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 Taxid562
    GeneSRM, SPS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPUTRESCINE AMINOPROPYLTRANSFERASE, SPDSY

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MTA2Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
2SPD2Ligand/IonSPERMIDINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:23 , VAL A:68 , ILE A:69 , GLN A:70 , TYR A:79 , GLN A:80 , ASP A:104 , ASP A:173 , SER A:174 , TYR A:241 , PRO A:242 , MTA A:501BINDING SITE FOR RESIDUE SPD A 601
2AC2SOFTWARETRP B:28 , VAL B:68 , GLN B:70 , TYR B:79 , GLN B:80 , ASP B:104 , ASP B:173 , SER B:174 , ASP B:176 , TYR B:241 , MTA B:501 , HOH B:603 , HOH B:605BINDING SITE FOR RESIDUE SPD B 601
3AC3SOFTWAREGLN A:49 , LEU A:65 , GLY A:101 , GLY A:103 , ASP A:104 , CYS A:123 , GLU A:124 , ILE A:125 , VAL A:129 , GLY A:154 , ASP A:155 , GLY A:156 , ASP A:173 , SER A:175 , SPD A:601BINDING SITE FOR RESIDUE MTA A 501
4AC4SOFTWAREGLN B:49 , LEU B:65 , GLY B:101 , GLY B:103 , ASP B:104 , CYS B:123 , GLU B:124 , ILE B:125 , ASP B:126 , VAL B:129 , GLY B:154 , ASP B:155 , GLY B:156 , ASP B:173 , PRO B:180 , ALA B:181 , SER B:183 , SPD B:601BINDING SITE FOR RESIDUE MTA B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O07)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O07)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011807L149VSPEE_HUMANPolymorphism1049932A/BL149V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_HUMAN18-253
 
  2A:18-253
B:18-253
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_HUMAN97-110
 
  2A:97-110
B:97-110

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003769571aENSE00001836529chr1:11120081-11119834248SPEE_HUMAN1-56562A:16-56
B:15-56
41
42
1.2cENST000003769572cENSE00000743131chr1:11119402-11119282121SPEE_HUMAN56-96412A:56-96
B:56-96
41
41
1.3aENST000003769573aENSE00000743128chr1:11118949-1111885793SPEE_HUMAN97-127312A:97-127
B:97-127
31
31
1.4bENST000003769574bENSE00000743127chr1:11116814-11116661154SPEE_HUMAN128-179522A:128-175
B:128-179
48
52
1.5ENST000003769575ENSE00000743125chr1:11116151-1111606884SPEE_HUMAN179-207292A:187-207
B:179-207
21
29
1.6bENST000003769576bENSE00000743124chr1:11115983-11115838146SPEE_HUMAN207-255492A:207-255
B:207-255
49
49
1.7bENST000003769577bENSE00000743123chr1:11115141-11115019123SPEE_HUMAN256-296412A:256-296
B:256-296
41
41
1.7dENST000003769577dENSE00001847545chr1:11114942-11114646297SPEE_HUMAN297-30262A:297-300
B:297-299
4
3

(-) 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:274
 aligned with SPEE_HUMAN | P19623 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:285
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     
           SPEE_HUMAN    16 IREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALND 300
               SCOP domains d2o07a_ A: Spermidine synthase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----------------------------------------------------------2o07A02 A:75-300 Vaccinia Virus protein VP39                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ee..eeee.......eeeeeeeeeeeeeeeee..eeeeeee....eeeee..eeeee...hhhhhhhhhhhhhh......eeeeeeee.hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhh....eeeeeee..-----------hhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhh.eeeeeeee...hhh.eeeeeeee..............hhhhhhhh.....hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PABS_2  PDB: A:18-253 UniProt: 18-253                                                                                                                                                                                                       ----------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------PABS_1        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:16-56 UniProt: 1-56    ----------------------------------------Exon 1.3a  PDB: A:97-127       Exon 1.4b  PDB: A:128-175 UniProt: 128-179          ---------------------------Exon 1.6b  PDB: A:207-255 UniProt: 207-255       Exon 1.7b  PDB: A:256-296                1.7d Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2c  PDB: A:56-96 UniProt: 56-96   ----------------------------------------------------------------------------------Exon 1.5  PDB: A:187-207     --------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2o07 A  16 IREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSS-----------ESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALND 300
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175         - |     195       205       215       225       235       245       255       265       275       285       295     
                                                                                                                                                                                         175         187                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with SPEE_HUMAN | P19623 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:285
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     
           SPEE_HUMAN    15 AIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALN 299
               SCOP domains d2o07b_ B: Spermidine synthase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------2o07B02 B:75-299 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeee.......eeeeeeeeeeeeeeeee..eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeeeee.hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhhhhh.....hhhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---PABS_2  PDB: B:18-253 UniProt: 18-253                                                                                                                                                                                                       ---------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: B:15-56 UniProt: 1-56     ----------------------------------------Exon 1.3a  PDB: B:97-127       Exon 1.4b  PDB: B:128-179 UniProt: 128-179          ---------------------------Exon 1.6b  PDB: B:207-255 UniProt: 207-255       Exon 1.7b  PDB: B:256-296                1.7 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.2c  PDB: B:56-96 UniProt: 56-96   ----------------------------------------------------------------------------------Exon 1.5  PDB: B:179-207     -------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2o07 B  15 AIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALN 299
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     

   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, 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 2O07)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPEE_HUMAN | P19623)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0006595    polyamine metabolic process    The chemical reactions and pathways involving 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/Swiss-Prot
        SPEE_HUMAN | P196232o05 2o06 2o0l 3rw9

(-) Related Entries Specified in the PDB File

2o05 CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH 5-METHYLTHIOADENOSINE
2o06 CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH 5-METHYLTHIOADENOSINE AND 1,4-DIAMINOBUTANE
2o0l CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH DECARBOXYLATED S-ADENOSYLMETHIONINE