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Protein

S-adenosylmethionine decarboxylase proenzyme

Gene

amd1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Essential for biosynthesis of the polyamines spermidine and spermine. Promotes maintenance and self-renewal of embryonic stem cells, by maintaining spermine levels.

Catalytic activityi

S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO2.

Cofactori

pyruvateNote: Binds 1 pyruvoyl group covalently per subunit.

Pathwayi: S-adenosylmethioninamine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes S-adenosylmethioninamine from S-adenosyl-L-methionine.
Proteins known to be involved in this subpathway in this organism are:
  1. S-adenosylmethionine decarboxylase proenzyme (amd1)
This subpathway is part of the pathway S-adenosylmethioninamine biosynthesis, which is itself part of Amine and polyamine biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes S-adenosylmethioninamine from S-adenosyl-L-methionine, the pathway S-adenosylmethioninamine biosynthesis and in Amine and polyamine biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei12 – 121By similarity
Active sitei15 – 151By similarity
Active sitei70 – 701Schiff-base intermediate with substrate; via pyruvic acidBy similarity
Active sitei84 – 841Proton donor; for catalytic activityBy similarity
Active sitei231 – 2311Proton acceptor; for processing activityBy similarity
Active sitei245 – 2451Proton acceptor; for processing activityBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Polyamine biosynthesis, Spermidine biosynthesis

Keywords - Ligandi

Pyruvate, S-adenosyl-L-methionine, Schiff base

Enzyme and pathway databases

UniPathwayiUPA00331; UER00451.

Names & Taxonomyi

Protein namesi
Recommended name:
S-adenosylmethionine decarboxylase proenzyme (EC:4.1.1.50)
Short name:
AdoMetDC
Short name:
SAMDC
Cleaved into the following 2 chains:
Gene namesi
Name:amd1
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-484615. amd1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 6969S-adenosylmethionine decarboxylase beta chainPRO_0000029971Add
BLAST
Chaini70 – 335266S-adenosylmethionine decarboxylase alpha chainPRO_0000029972Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei70 – 701Pyruvic acid (Ser); by autocatalysisBy similarity

Post-translational modificationi

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 (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei69 – 702Cleavage (non-hydrolytic); by autolysisBy similarity

Keywords - PTMi

Autocatalytic cleavage, Zymogen

Expressioni

Developmental stagei

First expressed at stage I of oocyte development, and is maximally expressed at stage II. Levels decline during oocyte maturation and after fertilization, and also in the early neurula. Levels increase dramatically during the late neurula stage reaching a maximum at the tail bud stage.

Structurei

3D structure databases

ProteinModelPortaliP79888.
SMRiP79888. Positions 8-329.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the eukaryotic AdoMetDC family.Curated

Phylogenomic databases

HOVERGENiHBG000761.
KOiK01611.

Family and domain databases

Gene3Di3.60.90.10. 1 hit.
InterProiIPR001985. S-AdoMet_decarboxylase.
IPR018167. S-AdoMet_decarboxylase_subgr.
IPR016067. S-AdoMet_deCO2ase_core.
IPR018166. S-AdoMet_deCO2ase_CS.
[Graphical view]
PANTHERiPTHR11570. PTHR11570. 1 hit.
PfamiPF01536. SAM_decarbox. 1 hit.
[Graphical view]
PIRSFiPIRSF001355. S-AdenosylMet_decarboxylase. 1 hit.
SUPFAMiSSF56276. SSF56276. 1 hit.
TIGRFAMsiTIGR00535. SAM_DCase. 1 hit.
PROSITEiPS01336. ADOMETDC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P79888-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMEESAAHF FEGTEKLLEL WFSQQDASKG SGDLRDIPRF EWDKLLENVH
60 70 80 90 100
CLIISVTKTD KQEAYVLSES SMFVSKRRFI LKTCGTTLLL QALVPLLELA
110 120 130 140 150
REYCGFDGIQ NFFYSRKNFM KPNHQEYPHR NFHEEVEFLN QIFPNGAAYC
160 170 180 190 200
MGRINSDCWY LYTLDIPDEY VISQPDQTLE ILMSELDPEV MDQFYMKEGV
210 220 230 240 250
TANDVTRVSG IRDLITGSVI DATMFSPCGY SMNGMKSDGT YWTIHITPEP
260 270 280 290 300
DFSYVSFETN VSLTTYDDLI SKVVDVFKPR KFVTTLFVNQ SSKCRTTFSC
310 320 330
AQKIEGFRRV DRQFAQFNDY NFVFTSFAKI QPQQS
Length:335
Mass (Da):38,819
Last modified:May 1, 1997 - v1
Checksum:iBA158A226F21F28C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S82621 mRNA. Translation: AAB36519.1.
BC042281 mRNA. Translation: AAH42281.1.
PIRiS72197.
RefSeqiNP_001080360.1. NM_001086891.1.
UniGeneiXl.7078.

Genome annotation databases

GeneIDi380052.
KEGGixla:380052.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S82621 mRNA. Translation: AAB36519.1.
BC042281 mRNA. Translation: AAH42281.1.
PIRiS72197.
RefSeqiNP_001080360.1. NM_001086891.1.
UniGeneiXl.7078.

3D structure databases

ProteinModelPortaliP79888.
SMRiP79888. Positions 8-329.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi380052.
KEGGixla:380052.

Organism-specific databases

CTDi262.
XenbaseiXB-GENE-484615. amd1.

Phylogenomic databases

HOVERGENiHBG000761.
KOiK01611.

Enzyme and pathway databases

UniPathwayiUPA00331; UER00451.

Family and domain databases

Gene3Di3.60.90.10. 1 hit.
InterProiIPR001985. S-AdoMet_decarboxylase.
IPR018167. S-AdoMet_decarboxylase_subgr.
IPR016067. S-AdoMet_deCO2ase_core.
IPR018166. S-AdoMet_deCO2ase_CS.
[Graphical view]
PANTHERiPTHR11570. PTHR11570. 1 hit.
PfamiPF01536. SAM_decarbox. 1 hit.
[Graphical view]
PIRSFiPIRSF001355. S-AdenosylMet_decarboxylase. 1 hit.
SUPFAMiSSF56276. SSF56276. 1 hit.
TIGRFAMsiTIGR00535. SAM_DCase. 1 hit.
PROSITEiPS01336. ADOMETDC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Maternal and zygotic expression of mRNA for S-adenosylmethionine decarboxylase and its relevance to the unique polyamine composition in Xenopus oocytes and embryos."
    Shinga J., Kashiwagi K., Tashiro K., Igarashi K., Shiokawa K.
    Biochim. Biophys. Acta 1308:31-40(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Tail bud.
  2. NIH - Xenopus Gene Collection (XGC) project
    Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.

Entry informationi

Entry nameiDCAM_XENLA
AccessioniPrimary (citable) accession number: P79888
Secondary accession number(s): Q5D0C5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 1, 1997
Last modified: October 14, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

It is uncertain whether Met-1 or Met-3 is the initiator.Curated

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.