1TMI - JenaLib

Title :   STRUCTURE OF THERMOTOGA MARITIMA S63A NON-PROCESSING MUTANT S-ADENOSYLMETHIONINE DECARBOXYLASE

Authors :   A. V. Toms, C. Kinsland, D. E. Mccloskey, A. E. Pegg, S. E. Ealick

Date :   10 Jun 04 (Deposition) - 29 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Two-Layer Alpha Beta-Sandwich, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. V. Toms, C. Kinsland, D. E. Mccloskey, A. E. Pegg, S. E. Ealick
Evolutionary Links As Revealed By The Structure Of Thermotoga Maritima S-Adenosylmethionine Decarboxylase.
J. Biol. Chem. V. 279 33837 2004
PubMed-ID: 15150268 | Reference-DOI: 10.1074/JBC.M403369200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:117
 aligned with SPEH_THEMA | Q9WZC3 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           SPEH_THEMA     2 KSLGRHLVAEFYECDREVLDNVQLIEQEMKQAAYESGATIVTSTFHRFLPYGVSGVVVISESHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEI 118
               SCOP domains d1tmia_ A: S-adenosylmethionine decarboxylase (SamDC, SpeH)                                                           SCOP domains
               CATH domains 1tmiA00 A:2-118 S-adenosylmethionine decarboxylase                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee..eeeeeeeehhhheeeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmi A   2 KSLGRHLVAEFYECDREVLDNVQLIEQEMKQAAYESGATIVTSTFHRFLPYGVSGVVVISEAHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEI 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with SPEH_THEMA | Q9WZC3 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           SPEH_THEMA     2 KSLGRHLVAEFYECDREVLDNVQLIEQEMKQAAYESGATIVTSTFHRFLPYGVSGVVVISESHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEI 118
               SCOP domains d1tmib_ B: S-adenosylmethionine decarboxylase (SamDC, SpeH)                                                           SCOP domains
               CATH domains 1tmiB00 B:2-118 S-adenosylmethionine decarboxylase                                                                    CATH domains
           Pfam domains (1) -----AdoMet_dc-1tmiB01 B:7-113                                                                                  ----- Pfam domains (1)
           Pfam domains (2) -----AdoMet_dc-1tmiB02 B:7-113                                                                                  ----- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee..eeeeeeeehhhheeeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmi B   2 KSLGRHLVAEFYECDREVLDNVQLIEQEMKQAAYESGATIVTSTFHRFLPYGVSGVVVISEAHLTIHTWPEYGYAAIDLFTCGEDVDPWKAFEHLKKALKAKRVHVVEHERGRYDEI 118
                                    11        21        31        41        51        61        71        81        91       101       111

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)

CATH Domains (1, 2)

Pfam Domains (1, 2)

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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1tmi)

	Sites
(no "Sites" information available for 1tmi)

	Cis Peptide Bonds
		Leu B:50 - Pro B:51	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1tmi
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SPEH_THEMA \| Q9WZC3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.1.1.50
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description