Q9WZC3 (SPEH_THEMA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
S-adenosylmethionine decarboxylase proenzyme
Short name=AdoMetDC
Short name=SAMDC
EC=4.1.1.50

Cleaved into the following 2 chains:

1. S-adenosylmethionine decarboxylase beta chain
2. S-adenosylmethionine decarboxylase alpha chain

Gene names

Name:	speH
Ordered Locus Names:	TM_0655

Organism

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) [Reference proteome] [HAMAP]

Taxonomic identifier

243274 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Thermotogae › Thermotogae › Thermotogales › Thermotogaceae › Thermotoga › Thermotoga maritima

Protein attributes

Sequence length	130 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine By similarity. HAMAP-Rule MF_00464
Catalytic activity	S-adenosyl-L-methionine = (5-deoxy-5-adenosyl)(3-aminopropyl)-methylsulfonium salt + CO2. HAMAP-Rule MF_00464
Cofactor	Pyruvoyl group Probable.
Pathway	Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from S-adenosyl-L-methionine: step 1/1. HAMAP-Rule MF_00464
Subunit structure	Heterotetramer of two alpha and two beta chains arranged as a dimer of alpha/beta heterodimers. Ref.2
Post-translational modification	Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain Probable. HAMAP-Rule MF_00464
Sequence similarities	Belongs to the prokaryotic AdoMetDC family. Type 1 subfamily.

Ontologies

Keywords
Biological process	Polyamine biosynthesis Spermidine biosynthesis
Ligand	Pyruvate S-adenosyl-L-methionine Schiff base
Molecular function	Decarboxylase Lyase
PTM	Autocatalytic cleavage Zymogen
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	S-adenosylmethioninamine biosynthetic process Inferred from electronic annotation. Source: HAMAP spermidine biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular_function	adenosylmethionine decarboxylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 62

62

S-adenosylmethionine decarboxylase beta chain Probable

PRO_0000030123

Chain

63 – 130

68

S-adenosylmethionine decarboxylase alpha chain Probable

PRO_0000030124

Sites

Active site

63

1

Schiff-base intermediate with substrate; via pyruvic acid By similarity

Active site

68

1

Proton acceptor; for processing activity Probable

Active site

83

1

Proton donor; for catalytic activity Probable

Site

62 – 63

2

Cleavage (non-hydrolytic); by autolysis Probable

Amino acid modifications

Modified residue

63

1

Pyruvic acid (Ser); by autocatalysis Probable

Experimental info

Mutagenesis

55

1

S → A: Cleaves more rapidly than the wild-type. Ref.2

Mutagenesis

63

1

S → A: Loss of processing. Ref.2

Mutagenesis

68

1

H → A: Cleaves much more slowly than the wild-type, but the addition of hydroxylamine which is known to cleave ester bonds leads to the cleavage of this mutant. Ref.2

Mutagenesis

83

1

C → A: Cleaves more rapidly than the wild-type. Ref.2

Secondary structure

1

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130

Helix Strand Turn

Details...

Beta strand

3 – 14

12

Helix

17 – 20

4

Helix

23 – 37

15

Beta strand

41 – 48

8

Beta strand

50 – 52

3

Beta strand

54 – 60

7

Beta strand

63 – 70

8

Helix

71 – 73

3

Beta strand

75 – 84

10

Helix

89 – 100

12

Beta strand

103 – 114

12

Helix

115 – 118

4

Sequences

	Sequence		Length	Mass (Da)
	Q9WZC3 [UniParc]. Last modified November 1, 1999. Version 1. Checksum: 7659FE20A2019928	FASTA	130	14,785
	10 20 30 40 50 60 MKSLGRHLVA EFYECDREVL DNVQLIEQEM KQAAYESGAT IVTSTFHRFL PYGVSGVVVI 70 80 90 100 110 120 SESHLTIHTW PEYGYAAIDL FTCGEDVDPW KAFEHLKKAL KAKRVHVVEH ERGRYDEIGI 130 PEDSPHKAAV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima." Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A., Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M., Cotton M.D., Pratt M.S. , Phillips C.A., Richardson D.L., Heidelberg J.F., Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M. Nature 399:323-329(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
[2]	"Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase." Toms A.V., Kinsland C., McCloskey D.E., Pegg A.E., Ealick S.E. J. Biol. Chem. 279:33837-33846(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-63, SUBUNIT, SELF-PROCESSING, ACTIVE SITES, MUTAGENESIS OF SER-55; SER-63; HIS-68 AND CYS-83.
[3]	"Crystal structure of S-adenosylmethionine decarboxylase proenzyme (tm0655) from Thermotoga maritima at 1.2-A resolution." Joint center for structural genomics (JCSG) Submitted (MAR-2005) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000512 Genomic DNA. Translation: AAD35739.1.

PIR

D72348.

RefSeq

NP_228464.1. NC_000853.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TLU	X-ray	1.55	A/B	1-130	[»]
1TMI	X-ray	1.70	A/B	1-130	[»]
1VR7	X-ray	1.20	A/B	1-130	[»]
3IWB	X-ray	2.06	A/C	64-130	[»]
			B/D	1-62	[»]
3IWC	X-ray	1.90	A/C	64-130	[»]
			B/D	1-62	[»]
3IWD	X-ray	1.90	A/C	64-130	[»]
			B/D	1-62	[»]

ProteinModelPortal

Q9WZC3.

SMR

Q9WZC3. Positions 2-121.

ModBase

Search...

Protein-protein interaction databases

STRING

243274.TM0655.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD35739; AAD35739; TM_0655.

GeneID

897764.

KEGG

tma:TM0655.

PATRIC

23936224. VBITheMar51294_0665.

Phylogenomic databases

eggNOG

COG1586.

KO

K01611.

OMA

AAMDIFT.

ProtClustDB

CLSK875272.

Enzyme and pathway databases

UniPathway

UPA00331; UER00451.

Family and domain databases

Gene3D

3.60.90.10. 1 hit.

HAMAP

MF_00464. AdoMetDC_1.

InterPro

IPR003826. S-AdoMet_decarboxylase-bac/arc.
IPR016067. S-AdoMet_deCO2ase_core.
IPR017716. S-AdoMet_deCOase_pro-enz.
[Graphical view]

Pfam

PF02675. AdoMet_dc. 1 hit.
[Graphical view]

SUPFAM

SSF56276. S-AdenosylMet_decarbase_core. 1 hit.

TIGRFAMs

TIGR03330. SAM_DCase_Bsu. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9WZC3.

Entry information

Entry name

SPEH_THEMA

Accession

Primary (citable) accession number: Q9WZC3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 24, 2001
Last sequence update:	November 1, 1999
Last modified:	May 1, 2013
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program