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(-) Description

Title :  CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM THERMOTOGA MARITIMA
 
Authors :  S. Korolev, T. Skarina, Y. Ikeguchi, A. E. Pegg, A. Joachimiak, A. Edwar A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  14 May 01  (Deposition) - 21 Nov 01  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Barrel, Rossmann Fold, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Korolev, Y. Ikeguchi, T. Skarina, S. Beasley, C. Arrowsmith, A. Edwards, A. Joachimiak, A. E. Pegg, A. Savchenko
The Crystal Structure Of Spermidine Synthase With A Multisubstrate Adduct Inhibitor.
Nat. Struct. Biol. V. 9 27 2002
PubMed-ID: 11731804  |  Reference-DOI: 10.1038/NSB737

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: PUTRESCINE AMINOPROPYLTRANSFERASE

 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 1INL)

(-) Sites  (0, 0)

(no "Site" information available for 1INL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_THEMA16-251
 
 
 		  4A:16-251
B:16-251
C:16-251
D:16-251
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_THEMA94-107
 
 
 		  4A:94-107
B:94-107
C:94-107
D:94-107

(-) Exons   (0, 0)

(no "Exon" information available for 1INL)

(-) 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:285
 aligned with SPEE_THEMA | Q9WZC2 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:295
                                    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       281       291     
           SPEE_THEMA     2 RTLKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDSTDPTAGQGGHLFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
               SCOP domains d1inla_ A: Spermidine synthase                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1inlA02 A:2-67  [code=2.30.140.10, no name defined]               1inlA01 A:68-296 Vaccinia Virus protein VP39                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........eeeeee.....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh...eeeeeee.----------..hhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee.......eeeeeeee.........hhhhhhh........hhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PABS_2  PDB: A:16-251 UniProt: 16-251                                                                                                                                                                                                       --------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1inl A   2 RTLKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDS----------LFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         -|      191       201       211       221       231       241       251       261       271       281       291     
                                                                                                                                                                                                   171        182                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with SPEE_THEMA | Q9WZC2 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:295
                                    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       281       291     
           SPEE_THEMA     2 RTLKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDSTDPTAGQGGHLFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
               SCOP domains d1inlb_ B: Spermidine synthase                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1inlB02 B:2-67  [code=2.30.140.10, no name defined]               1inlB01 B:68-296 Vaccinia Virus protein VP39                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........eeeeee.....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh......eeeee.hhhhhhh.....eeeeee.......----...hhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhh...eeeeeeee.......eeeeeeee.........hhhhhhh........hhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PABS_2  PDB: B:16-251 UniProt: 16-251                                                                                                                                                                                                       --------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1inl B   2 RTLKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDSTDPTA----HLFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
                                    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       281       291     
                                                                                                                                                                                                        176  181                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:293
 aligned with SPEE_THEMA | Q9WZC2 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
           SPEE_THEMA     4 LKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDSTDPTAGQGGHLFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
               SCOP domains d1inlc_ C: Spermidine synthase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1inlC02 C:4-67  [code=2.30.140.10, no name defined]             1inlC01 C:68-296 Vaccinia Virus protein VP39                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh......eeeee.hhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee.......eeeeeeee.........hhhhhhh........hhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------PABS_2  PDB: C:16-251 UniProt: 16-251                                                                                                                                                                                                       --------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1inl C   4 LKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDSTDPTAGQGGHLFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   


Chain D from PDB  Type:PROTEIN  Length:282
 aligned with SPEE_THEMA | Q9WZC2 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
           SPEE_THEMA     4 LKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDSTDPTAGQGGHLFTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
               SCOP domains d1inld_ D: Spermidine synthase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1inlD02 D:4-67  [code=2.30.140.10, no name defined]             1inlD01 D:68-296 Vaccinia Virus protein VP39                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhh..hhhhh....eeeee.hhhhhhhhh...eeeeeee.-----------.hhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee.......eeeeeeee.........hhhhhhh........hhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------PABS_2  PDB: D:16-251 UniProt: 16-251                                                                                                                                                                                                       --------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1inl D   4 LKELERELQPRQHLWYFEYYTGNNVGLFMKMNRVIYSGQSDIQRIDIFENPDLGVVFALDGITMTTEKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKHDSVEKAILCEVDGLVIEAARKYLKQTSCGFDDPRAEIVIANGAEYVRKFKNEFDVIIIDS-----------FTEEFYQACYDALKEDGVFSAETEDPFYDIGWFKLAYRRISKVFPITRVYLGFMTTYPSGMWSYTFASKGIDPIKDFDPEKVRKFNKELKYYNEEVHVASFALPNFVKKELGLM 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       | -       183       193       203       213       223       233       243       253       263       273       283       293   
                                                                                                                                                                                                 171         183
   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 1INL)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SPEE_THEMA | Q9WZC2)
molecular function
    GO:0043919    agmatine aminopropyltransferase activity    Catalysis of the reaction: agmatine + S-adenosylmethioninamine = N1-aminopropylagmatine + 5'-methylthioadenosine.
    GO:0043918    cadaverine aminopropyltransferase activity    Catalysis of the reaction: S-adenosylmethioninamine + cadaverine = 5'-methylthioadenosine + N-(3-aminopropyl)cadaverine.
    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:0050314    sym-norspermidine synthase activity    Catalysis of the reaction: 1,3-diaminopropane + S-adenosylmethioninamine = S-methyl-5'-thioadenosine + bis(3-aminopropyl)amine + H(+).
    GO:0010487    thermospermine synthase activity    Catalysis of the reaction: S-adenosyl-L-methioninamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SPEE_THEMA | Q9WZC2: 1jq3

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