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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME (TM0655) FROM THERMOTOGA MARITIMA AT 1.2 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 Feb 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm0655, S-Adenosylmethionine Decarboxylase Proenzyme, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of S-Adenosylmethionine Decarboxylase Proenzyme (Tm0655) From Thermotoga Maritima At 1. 2 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME
    Chains: A, B
    EC Number: 4.1.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0655
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: ADOMETDC, SAMDC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:9 , GLU A:11 , HIS A:106 , HIS B:110BINDING SITE FOR RESIDUE EDO A 131

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VR7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:50 -Pro A:51
2Pro A:51 -Tyr A:52
3Leu B:50 -Pro B:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VR7)

(-) Exons   (0, 0)

(no "Exon" information available for 1VR7)

(-) 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:120
 aligned with SPEH_THEMA | Q9WZC3 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
           SPEH_THEMA     2 KSLGRHLVAEFYECDREVLDNVQLIEQEMKQAAYESGATIVTSTFHRFLPYGVSGVVVISESHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEIGIP 121
               SCOP domains d1vr7a_ A: automated matches                                                                                             SCOP domains
               CATH domains 1vr7A00 A:2-121 S-adenosylmethionine decarboxylase                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee..eeeeeeeehhhheeeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vr7 A   2 KSLGRHLVAEFYECDREVLDNVQLIEQEmKQAAYESGATIVTSTFHRFLPYGVSGVVVISESHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEIGIP 121
                                    11        21        31        41        51        61        71        81        91       101       111       121
                                                       30-MSE                                                                                       


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with SPEH_THEMA | Q9WZC3 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
           SPEH_THEMA     1 MKSLGRHLVAEFYECDREVLDNVQLIEQEMKQAAYESGATIVTSTFHRFLPYGVSGVVVISESHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEI 118
               SCOP domains d1vr7b_ B: automated matches                                                                                           SCOP domains
               CATH domains -1vr7B00 B:2-118 S-adenosylmethionine decarboxylase                                                                    CATH domains
           Pfam domains (1) ------AdoMet_dc-1vr7B01 B:7-113                                                                                  ----- Pfam domains (1)
           Pfam domains (2) ------AdoMet_dc-1vr7B02 B:7-113                                                                                  ----- Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...eeeeeeehhhheeeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1vr7 B   1 mKSLGRHLVAEFYECDREVLDNVQLIEQEmKQAAYESGATIVTSTFHRFLPYGVSGVVVISESHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEI 118
                            |       10        20        30        40        50        60        70        80        90       100       110        
                            1-MSE                       30-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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: AdoMet_dc] (3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPEH_THEMA | Q9WZC3)
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.

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 Related Entries

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        SPEH_THEMA | Q9WZC3: 1tlu 1tmi 3iwb 3iwc 3iwd

(-) Related Entries Specified in the PDB File

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