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(-) Description

Title :  CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM HELICOBACTER PYLORI
 
Authors :  Y. -J. Sun, P. -K. Lu
Date :  08 May 06  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Putrescine Aminopropyltransferase, Spermidine Synthase, Spermidine Biosynthesis, Polyamine Biosynthesis, Spee (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. -K. Lu, J. -Y. Tsai, H. Y. Chien, H. Huang, C. -H. Chu, Y. -J. Sun
Crystal Structure Of Helicobacter Pylori Spermidine Synthase: A Rossmann-Like Fold With A Distinct Active Site
Proteins: Struct. , Funct. , V. 67 743 2007 Bioinf.
PubMed-ID: 17357156  |  Reference-DOI: 10.1002/PROT.21315

(-) Compounds

Molecule 1 - SPERMIDINE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: PUTRESCINE AMINOPROPYLTRANSFERASE, SPDSY

 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 2CMG)

(-) Sites  (0, 0)

(no "Site" information available for 2CMG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CMG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CMG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CMG)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PABS_2PS51006 Polyamine biosynthesis (PABS) domain profile.SPEE_HELPY1-249
 		  2A:1-249
B:1-249

(-) Exons   (0, 0)

(no "Exon" information available for 2CMG)

(-) 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:262
 aligned with SPEE_HELPY | O25503 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           SPEE_HELPY     1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
               SCOP domains d2cmga_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..eeeeeee....eeeeeee...eeeeee..eeee...hhhhhhhhhhhhhh......eeeee...hhhhhhhhh....eeeee..hhhhhhhhh....hhhhhhh...eeee.hhhhh....eeeeee....hhhhhhhhhh.eeeeeeeeeeee....hhhhhhhhhhhhhh...eeeee.........eeeeeee.........hhhhhh........hhhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PABS_2  PDB: A:1-249 UniProt: 1-249                                                                                                                                                                                                                      ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmg A   1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
                                    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  


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with SPEE_HELPY | O25503 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           SPEE_HELPY     1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
               SCOP domains d2cmgb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..eeeeeee....eeeeeee...eeeeee...eee...hhhhhhhhhhhhhh......eeeee...hhhhhhhhh....eeeee..hhhhhhhh.....hhhhhhhh..eeee.hhhhh....eeeeee....hhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhh...eeeee..........eeeeee.........hhhhhh........hhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PABS_2  PDB: B:1-249 UniProt: 1-249                                                                                                                                                                                                                      ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmg B   1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
                                    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
   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  (0, 0)

(no "CATH Domain" information available for 2CMG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CMG)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPEE_HELPY | O25503)
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.

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 Related Entries

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UniProtKB/Swiss-Prot
        SPEE_HELPY | O25503: 2cmh

(-) Related Entries Specified in the PDB File

2cmh CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM HELICOBACTER PYLORI