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(-) Description

Title :  CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE
 
Authors :  A. Y. Tan, P. C. Smith, J. Shen, R. Xiao, T. Acton, B. Rost, G. Montelione, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  26 Jul 02  (Deposition) - 30 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rossmann Fold, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Y. Tan, P. C. Smith, J. Shen, R. Xiao, T. Acton, B. Rost, G. Montelione, J. F. Hunt
Crystal Structure Of Spermidine Synthase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1IY9)

(-) Sites  (0, 0)

(no "Site" information available for 1IY9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IY9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IY9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IY9)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_BACSU3-236
 
 
 		  4A:3-236
B:1003-1236
C:2003-2236
D:3003-3236
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_BACSU80-93
 
 
 		  4A:80-93
B:1080-1093
C:2080-2093
D:3080-3093

(-) Exons   (0, 0)

(no "Exon" information available for 1IY9)

(-) 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_BACSU | P70998 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
          SPEE_BACSU      2 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI  275
               SCOP domains d1iy9a_ A: Spermidine synthase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1iy9A02 A:2-53  [code=2.30.140.10, no name defined] 1iy9A01 A:54-237 Vaccinia Virus protein VP39                                                                                                                                            -------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeeeeeeeeee....eeeeeee...eeeeee..eeeee...hhhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh......eeeee..hhhhhhh....eeeeee..............hhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeee....hhhhheeeeeee........hhhhh........hhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PABS_2  PDB: A:3-236 UniProt: 3-236                                                                                                                                                                                                       --------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1iy9 A    2 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI  275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with SPEE_BACSU | P70998 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
          SPEE_BACSU      2 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI  275
               SCOP domains d1iy9b_ B: Spermidine synthase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1iy9B02 B:1002-1053                                 1iy9B01 B:1054-1237 Vaccinia Virus protein VP39                                                                                                                                         -------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeeeeeeeeee....eeeeeee...eeeeee..eeeee...hhhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh......eeeee..hhhhhhh....eeeeee..............hhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeee....hhhhheeeeeee........hhhhh........hhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PABS_2  PDB: B:1003-1236 UniProt: 3-236                                                                                                                                                                                                   --------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1iy9 B 1002 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI 1275
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271    


Chain C from PDB  Type:PROTEIN  Length:274
 aligned with SPEE_BACSU | P70998 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
          SPEE_BACSU      2 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI  275
               SCOP domains d1iy9c_ C: Spermidine synthase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1iy9C02 C:2002-2053                                 1iy9C01 C:2054-2237 Vaccinia Virus protein VP39                                                                                                                                         -------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeeeeeeeeee....eeeeeee...eeeeee..eeeee...hhhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh......eeeee..hhhhhhh....eeeeee..............hhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeee....hhhhheeeeeee...hhhhhhhhhh........hhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PABS_2  PDB: C:2003-2236 UniProt: 3-236                                                                                                                                                                                                   --------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1iy9 C 2002 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI 2275
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251      2261      2271    


Chain D from PDB  Type:PROTEIN  Length:274
 aligned with SPEE_BACSU | P70998 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
          SPEE_BACSU      2 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI  275
               SCOP domains d1iy9d_ D: Spermidine synthase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1iy9D02 D:3002-3053                                 1iy9D01 D:3054-3237 Vaccinia Virus protein VP39                                                                                                                                         -------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeeeeeeeeee....eeeeeee...eeeeee..eeeee...hhhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh......eeeee..hhhhhhh....eeeeee..............hhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee...hhhhhhhhhh........hhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PABS_2  PDB: D:3003-3236 UniProt: 3-236                                                                                                                                                                                                   --------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1iy9 D 3002 SELWYTEKQTKNFGITMKVNKTLHTEQTEFQHLEMVETEEFGNMLFLDGMVMTSEKDEFVYHEMVAHVPLFTHPNPEHVLVVGGGDGGVIREILKHPSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDVQVDDGFMHIAKSENQYDVIMVDSTEPVGPAVNLFTKGFYAGIAKALKEDGIFVAQTDNPWFTPELITNVQRDVKEIFPITKLYTANIPTYPSGLWTFTIGSKKYDPLAVEDSRFFDIETKYYTKDIHKAAFVLPKFVSDLI 3275
                                  3011      3021      3031      3041      3051      3061      3071      3081      3091      3101      3111      3121      3131      3141      3151      3161      3171      3181      3191      3201      3211      3221      3231      3241      3251      3261      3271
   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, 4)

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

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IY9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SPEE_BACSU | P70998)
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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  1iy9
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 Related Entries

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