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(-) Description

Title :  CRYSTAL STRUCTURE OF POLYAMINE AMINOPROPYLTRANSFEASE FROM THERMUS THERMOPHILUS
 
Authors :  T. Ganbe, M. Ohnuma, T. Sato, T. Kumasaka, T. Oshima, N. Tanaka, Riken S Genomics/Proteomics Initiative (Rsgi)
Date :  18 Jul 03  (Deposition) - 05 Aug 03  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Spermidien Synthase, Spermine Synthase, Polyamine, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Ohnuma, T. Ganbe, Y. Terui, M. Niitsu, T. Sato, N. Tanaka, M. Tamakoshi, K. Samejima, T. Kumasaka, T. Oshima
Crystal Structures And Enzymatic Properties Of A Triamine/Agmatine Aminopropyltransferase From Thermus Thermophilus
J. Mol. Biol. V. 408 971 2011
PubMed-ID: 21458463  |  Reference-DOI: 10.1016/J.JMB.2011.03.025

(-) Compounds

Molecule 1 - POLYAMINE AMINOPROPYLTRANSFERASE
    ChainsA, B
    EC Number2.5.1.16, 2.5.1.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21C
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB
Biological Unit 2 (1x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1UIR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_THET84-241
 
  2A:4-241
B:4-241
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_THET881-94
 
  2A:81-94
B:81-94
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_THET84-241
 
  4A:4-241
B:4-241
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_THET881-94
 
  4A:81-94
B:81-94
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_THET84-241
 
  2A:4-241
B:4-241
2PABS_1PS01330 Polyamine biosynthesis (PABS) domain signature.SPEE_THET881-94
 
  2A:81-94
B:81-94

(-) Exons   (0, 0)

(no "Exon" information available for 1UIR)

(-) 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:309
 aligned with SPEE_THET8 | Q5SK28 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    10        20        30        40        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  
           SPEE_THET8     1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQAGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY 312
               SCOP domains d1uira_ A: Spermidine synthase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --1uirA01 A:3-54  [code=2.30.140.10, no name defined] -1uirA02 A:56-311 Vaccinia Virus protein VP39                                                                                                                                                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhhhheeeeeeeeeeeeee..---hhhhhhhhhhhh...eeeeeeee.hhhh.eeeeeeee..........hhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhh.........eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---PABS_2  PDB: A:4-241 UniProt: 4-241                                                                                                                                                                                                           ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1uir A   1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQTGMILL---RVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY 312
                                    10        20        30        40        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  
                                                                                                                                                                                                                                 200 204                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with SPEE_THET8 | Q5SK28 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    10        20        30        40        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   
           SPEE_THET8     1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQAGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPYK 313
               SCOP domains d1uirb_ B: Spermidine synthase                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --1uirB01 B:3-54  [code=2.30.140.10, no name defined] -1uirB02 B:56-311 Vaccinia Virus protein VP39                                                                                                                                                                                                                    -- CATH domains
           Pfam domains (1) ----Spermine_synth-1uirB01 B:5-248                                                                                                                                                                                                                      ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Spermine_synth-1uirB02 B:5-248                                                                                                                                                                                                                      ----------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeee....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeeee......hhhhhhhhhhhh...eeeeeeee.hhhh.eeeeeeee........hhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhh.........eee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PABS_2  PDB: B:4-241 UniProt: 4-241                                                                                                                                                                                                           ------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uir B   1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQTGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPYK 313
                                    10        20        30        40        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   

   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 Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SPEE_THET8 | Q5SK28)
molecular function
    GO:0043919    agmatine aminopropyltransferase activity    Catalysis of the reaction: agmatine + S-adenosylmethioninamine = N1-aminopropylagmatine + 5'-methylthioadenosine.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        SPEE_THET8 | Q5SK283anx

(-) Related Entries Specified in the PDB File

1inl
1iy9
1jq3
1mjf RELATED ID: TTK003000339.1 RELATED DB: TARGETDB