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(-) Description

Title :  PUTATIVE SPERMIDINE SYNTHETASE FROM PYROCOCCUS FURIOSUS PFU-132382
 
Authors :  Southeast Collaboratory For Structural Genomics (Secsg)
Date :  27 Aug 02  (Deposition) - 18 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrococcus Furiosus, Spermidine Synthetase, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Southeast Collaboratory For Structural Genomics
Putative Spermidine Synthetase From Pyrococcus Furiosus Pfu-132382
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1MJF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:184 -Pro A:185
2Ser A:228 -Pro A:229
3Asn B:184 -Pro B:185
4Ser B:228 -Pro B:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_PYRFU6-238
 		  2A:5-237
B:5-237
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_PYRFU79-92
 		  2A:78-91
B:78-91

(-) Exons   (0, 0)

(no "Exon" information available for 1MJF)

(-) 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:271
 aligned with SPEE_PYRFU | Q8U4G1 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:276
                                    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      
           SPEE_PYRFU     4 AFIEWYPRGYGVAFKIKKKIYEKLSKYQKIEVYETEGFGRLLALDGTVQLVTLGERSYHEPLVHPAMLAHPKPKRVLVIGGGDGGTVREVLQHDVDEVIMVEIDEDVIMVSKDLIKIDNGLLEAMLNGKHEKAKLTIGDGFEFIKNNRGFDVIIADSTDPVGPAKVLFSEEFYRYVYDALNNPGIYVTQAGSVYLFTDELISAYKEMKKVFDRVYYYSFPVIGYASPWAFLVGVKGDIDFTKIDRERAKKLQLEYYDPLMHETLFQMPKYIRETLQ 279
               SCOP domains d1mjfa_ A: Putative spermidine synthetase PF0127 (SpeE)                                                                                                                                                                                                                              SCOP domains
               CATH domains 1mjfA01 A:3-54  [code=2.30.140.10, no name defined] 1mjfA02 A:55-278 Vaccinia Virus protein VP39                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeee.eeeeeeeee....eeeeeee....eeeee..eeeee...hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh.....eeeeee.hhhhhhhhhhhh....hhhhhhhh.....eeeee.hhhhhhhhh..eeeeeee....-----...hhhhhhhhhhheeeeeeeeeeeee...hhhhhhhhhhhhhhhh.eeeeeee........eeeeeeee........hhhhhhh......hhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --PABS_2  PDB: A:5-237 UniProt: 6-238                                                                                                                                                                                                      ----------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mjf A   3 AFIEWYPRGYGVAFKIKKKIYEKLSKYQKIEVYETEGFGRLLALDGTVQLVTLGERSYHEPLVHPAMLAHPKPKRVLVIGGGDGGTVREVLQHDVDEVIMVEIDEDVIMVSKDLIKIDNGLLEAMLNGKHEKAKLTIGDGFEFIKNNRGFDVIIADSTDP-----VLFSEEFYRYVYDALNNPGIYVTQAGSVYLFTDELISAYKEMKKVFDRVYYYSFPVIGYASPWAFLVGVKGDIDFTKIDRERAKKLQLEYYDPLMHETLFQMPKYIRETLQ 278
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     | 172       182       192       202       212       222       232       242       252       262       272      
                                                                                                                                                                                         162   168                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:269
 aligned with SPEE_PYRFU | Q8U4G1 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:276
                                    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      
           SPEE_PYRFU     4 AFIEWYPRGYGVAFKIKKKIYEKLSKYQKIEVYETEGFGRLLALDGTVQLVTLGERSYHEPLVHPAMLAHPKPKRVLVIGGGDGGTVREVLQHDVDEVIMVEIDEDVIMVSKDLIKIDNGLLEAMLNGKHEKAKLTIGDGFEFIKNNRGFDVIIADSTDPVGPAKVLFSEEFYRYVYDALNNPGIYVTQAGSVYLFTDELISAYKEMKKVFDRVYYYSFPVIGYASPWAFLVGVKGDIDFTKIDRERAKKLQLEYYDPLMHETLFQMPKYIRETLQ 279
               SCOP domains d1mjfb_ B: Putative spermidine synthetase PF0127 (SpeE)                                                                                                                                                                                                                              SCOP domains
               CATH domains 1mjfB01 B:3-54  [code=2.30.140.10, no name defined] 1mjfB02 B:55-278 Vaccinia Virus protein VP39                                                                                                                                                                                     CATH domains
           Pfam domains (1) Spermine_synth-1mjfB01 B:3-248                                                                                                                                                                                                                        ------------------------------ Pfam domains (1)
           Pfam domains (2) Spermine_synth-1mjfB02 B:3-248                                                                                                                                                                                                                        ------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee...eeeee.eeeeeeeee....eeeeeee....eeeee..eeeee...hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh.....eeeeee.hhhhhhhhhhhh....hhhhhhhh.....eeeee......--....eeeeeee....-----...hhhhhhhhhhheeeeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeee........eeeeeeee........hhhhhh.......hhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --PABS_2  PDB: B:5-237 UniProt: 6-238                                                                                                                                                                                                      ----------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mjf B   3 AFIEWYPRGYGVAFKIKKKIYEKLSKYQKIEVYETEGFGRLLALDGTVQLVTLGERSYHEPLVHPAMLAHPKPKRVLVIGGGDGGTVREVLQHDVDEVIMVEIDEDVIMVSKDLIKIDNGLLEAMLNGKHEKAKLTIGDGFEF--NNRGFDVIIADSTDP-----VLFSEEFYRYVYDALNNPGIYVTQAGSVYLFTDELISAYKEMKKVFDRVYYYSFPVIGYASPWAFLVGVKGDIDFTKIDRERAKKLQLEYYDPLMHETLFQMPKYIRETLQ 278
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142  |  | 152       162     | 172       182       192       202       212       222       232       242       252       262       272      
                                                                                                                                                                        145  |           162   168                                                                                                              
                                                                                                                                                                           148
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPEE_PYRFU | Q8U4G1)
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.

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    Asn A:184 - Pro A:185   [ RasMol ]  
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1inl SEQUENCE HOMOLOG USED IN MOLECULAR REPLACEMENT. RELATED ID: PFU-132382-001 RELATED DB: TARGETDB