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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE DECARBOXYLASE FROM POTATO
 
Authors :  E. M. Bennett, J. L. Ekstrom, A. E. Pegg, S. E. Ealick
Date :  20 Aug 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Covalent Pyruvoyl Group, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Bennett, J. L. Ekstrom, A. E. Pegg, S. E. Ealick
Monomeric S-Adenosylmethionine Decarboxylase From Plants Provides An Alternative To Putrescine Stimulation
Biochemistry V. 41 14509 2002
PubMed-ID: 12463749  |  Reference-DOI: 10.1021/BI026710U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S-ADENOSYLMETHIONINE DECARBOXYLASE
    Chains: B
    EC Number: 4.1.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE31
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BETA CHAIN
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Synonym: ADOMETDC, SAMDC
 
Molecule 2 - S-ADENOSYLMETHIONINE DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE31
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ALPHA CHAIN
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Synonym: ADOMETDC, SAMDC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PYR1Mod. Amino AcidPYRUVIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1MHM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:231 -Pro A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOMETDCPS01336 S-adenosylmethionine decarboxylase signature.DCAM_SOLTU67-77  1B:67-72

(-) Exons   (0, 0)

(no "Exon" information available for 1MHM)

(-) 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:254
 aligned with DCAM_SOLTU | Q04694 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:265
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
           DCAM_SOLTU    73 SSLFVYSYKIIIKTCGTTKLLLAIPPILRLAETLSLKVQDVRYTRGSFIFPGAQSFPHRHFSEEVAVLDGYFGKLAAGSKAVIMGSPDKTQKWHVYSASAGSVQSNDPVYTLEMCMTGLDREKASVFYKTEESSAAHMTVRSGIRKILPKSEICDFEFEPCGYSMNSIEGAAVSTIHITPEDGFTYASFESVGYNPKTMELGPLVERVLACFEPAEFSVALHADVATKLLERICSVDVKGYSLAEWSPEEFGEGGSIVYQKFTRT 337
               SCOP domains d1mhm.1 B:,A: S-adenosylmethionine decarboxylas           e                                                                                                                                                                                                               SCOP domains
               CATH domains -1mhmA00 A:74-337 S-adenosylmethionine decarbox           ylase                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeee...hhhhhhhhhhhhhhhh...eeeeeeee..-----------.hhhhhhhhhhhhhh.....eeeeee........eeeeeee...........eeeeeeeeehhhhhhh.......hhhhhhhhhhhhhh....eeeeee.....eeeeeee..eeeeeeee......eeeeeee.......hhhhhhhhhhhhhheeeeeeeeee..hhhhhhhhhh.....eeeeeeeeee.hhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ADOME-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mhm A  73 xSLFVYSYKIIIKTCGTTKLLLAIPPILRLAETLSLKVQDVRYTRGS-----------RHFSEEVAVLDGYFGKLAAGSKAVIMGSPDKTQKWHVYSASAGSVQSNDPVYTLEMCMTGLDREKASVFYKTEESSAAHMTVRSGIRKILPKSEICDFEFEPCGYSMNSIEGAAVSTIHITPEDGFTYASFESVGYNPKTMELGPLVERVLACFEPAEFSVALHADVATKLLERICSVDVKGYSLAEWSPEEFGEGGSIVYQKFTRT 337
                            |       82        92       102       112      |  -       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
                            |                                           119         131                                                                                                                                                                                                              
                           73-PYR                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with DCAM_SOLTU | Q04694 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:58
                                    24        34        44        54        64        
           DCAM_SOLTU    15 FEKRLEISFVEPGLFADPNGKGLRSLSKAQLDEILGPAECTIVDNLSNDYVDSYVLSE  72
               SCOP domains d1mhm.1 B:,A: S    -adenosylmethionine decarboxylase       SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
           Pfam domains (1) SAM_decarbox-1m    hmB01 B:15-72                           Pfam domains (1)
           Pfam domains (2) SAM_decarbox-1m    hmB02 B:15-72                           Pfam domains (2)
         Sec.struct. author .eeeeeeee......----..hhhhhhhhhhhhhhhhhh.eeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------ADOMET PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1mhm B  15 FEKRLEISFVEPGLF----GKGLRSLSKAQLDEILGPAECTIVDNLSNDYVDSYVLSE  72
                                    24    |   34        44        54        64        
                                         29   34
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SAM_decarbox] (4)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DCAM_SOLTU | Q04694)
molecular function
    GO:0004014    adenosylmethionine decarboxylase activity    Catalysis of the reaction: S-adenosyl-L-methionine + H(+) = S-adenosylmethioninamine + CO(2).
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006557    S-adenosylmethioninamine biosynthetic process    The chemical reactions and pathways resulting in the formation of S-adenosylmethioninamine, (5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt.
    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.
    GO:0006597    spermine biosynthetic process    The chemical reactions and pathways resulting in the formation of spermine, a polybasic amine found in human sperm, in ribosomes and in some viruses and involved in nucleic acid packaging.

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(-) Related Entries Specified in the PDB File

1jen CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE DECARBOXYLASE FROM HUMAN