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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO FORM OF SPERMIDINE SYNTHASE FROM TRYPANOSOMA CRUZI AT 2.5 A RESOLUTION
 
Authors :  J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)
Date :  08 Jan 08  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Spermidine Synthase, Trypanosoma Cruzi, Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Structural Genomics Of Pathogenic Protozoa Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bosch, W. G. J. Hol
Crystal Structure Of Spermidine Synthase From Trypanosoma Cruzi.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector: T7 SYSTEM
    Expression System Vector Type: PLASMID
    Gene: TC00.1047053510339.50
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 353153
    Strain: CL BRENER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3BWB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BWB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BWB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BWB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BWB)

(-) Exons   (0, 0)

(no "Exon" information available for 3BWB)

(-) 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:288
 aligned with Q4DA73_TRYCC | Q4DA73 from UniProtKB/TrEMBL  Length:296

    Alignment length:291
                                    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 
         Q4DA73_TRYCC     4 SELISGGWFREENDQWPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWGTVMALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDNTYDVVIIDTTDPAGPASKLFGEAFYKDVLRILKPDGICCNQGESIWLDLELIEKMSRFIRETGFASVQYALMHVPTYPCGSIGTLVCSKKAGVDVTKPLRPVEDMPFAKDLKYYDSEMHKASFALPRFARHINN 294
               SCOP domains d3bwba_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -----------------------------------------------------------------3bwbA02 A:77-302 Vaccinia Virus protein VP39                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.......eeeeeeeeeeeeeee....eeeeeee.......eeeee..eeeee...hhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh.....eeeeeee....---....hhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...........eeeeee............hhhhh.hhhhh...hhhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwb A  12 SELISGGWFREENDQWPGQAmSLRVEKVLYDAPTKFQHLTIFESDPKGPWGTVmALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDIDGEVmEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDNTYDVVIIDTTDP---ASKLFGEAFYKDVLRILKPDGICCNQGESIWLDLELIEKmSRFIRETGFASVQYALmHVPTYPCGSIGTLVCSKKAGVDVTKPLRPVEDmPFAKDLKYYDSEmHKASFALPRFARHINN 302
                                    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       301 
                                               32-MSE                           65-MSE                                                            132-MSE                                         180 184                                    223-MSE          240-MSE                          273-MSE      286-MSE            


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with Q4DA73_TRYCC | Q4DA73 from UniProtKB/TrEMBL  Length:296

    Alignment length:287
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
         Q4DA73_TRYCC     8 SGGWFREENDQWPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWGTVMALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDNTYDVVIIDTTDPAGPASKLFGEAFYKDVLRILKPDGICCNQGESIWLDLELIEKMSRFIRETGFASVQYALMHVPTYPCGSIGTLVCSKKAGVDVTKPLRPVEDMPFAKDLKYYDSEMHKASFALPRFARHINN 294
               SCOP domains d3bwbb_ B: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------3bwbB02 B:77-302 Vaccinia Virus protein VP39                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee........eeeeeeeeeeeeeee....eeeeeee.......eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh.....eeeeeee......----.hhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...........eeeeee............hhhhhhhhhhh...hhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwb B  16 SGGWFREENDQWPGQAmSLRVEKVLYDAPTKFQHLTIFESDPKGPWGTVmALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLREVLRHGTVEHCDLVDIDGEVmEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDNTYDVVIIDTTDPAG----LFGEAFYKDVLRILKPDGICCNQGESIWLDLELIEKmSRFIRETGFASVQYALmHVPTYPCGSIGTLVCSKKAGVDVTKPLRPVEDmPFAKDLKYYDSEmHKASFALPRFARHINN 302
                                    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       
                                           32-MSE                           65-MSE                                                            132-MSE                                           182  187                                 223-MSE          240-MSE                          273-MSE      286-MSE
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BWB)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4DA73_TRYCC | Q4DA73)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q4DA73_TRYCC | Q4DA73: 3bwc 4yuv 4yuw 4yux 4yuy 4yuz 4yv0 4yv1 4yv2 5b1s

(-) Related Entries Specified in the PDB File

3bwc CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM TRYPANOSOMA CRUZI IN COMPLEX WITH SAM