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Protein

S-adenosylmethionine decarboxylase proenzyme

Gene

speD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

Catalytic activityi

S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO2.1 Publication

Cofactori

pyruvate3 PublicationsNote: Binds 1 pyruvoyl group covalently per subunit.3 Publications

Enzyme regulationi

Allosterically activated by metal cations, which are absolutely required for activity. The presumed physiological activator is Mg2+, but can also be activated in vitro by other divalent cations such as Mn2+, Fe2+ and Ca2+, by the monovalent cation Li+, and by trivalent cations such as Eu3+, Tb3+ and Gd3+. Competitively inhibited by methylglyoxal bis-guanylhydrazone. Also inhibited by Zn2+, inhibition may be due to interaction with the active site cysteine. Inactivated by treatment with the imine reductant NaCNBH3 only in the presence of substrate.3 Publications

Kineticsi

  1. KM=60 µM for S-adenosyl-L-methionine (at 25 degrees Celsius in the presence of 0.01 M MgCl2)1 Publication
  1. Vmax=3.8 µmol/min/mg enzyme (at 25 degrees Celsius in the presence of 0.01M MgCl2)1 Publication
  2. Vmax=6.8 µmol/min/mg enzyme (at 37 degrees Celsius in the presence of 0.1M MgCl2)1 Publication

pH dependencei

Optimum pH is 7.4. Active from pH 6.7 to 8.5.2 Publications

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 (speD)
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)DescriptionActionsGraphical viewLength
Active sitei112Schiff-base intermediate with substrate; via pyruvic acid1
Active sitei117Proton acceptor; for processing activityBy similarity1
Active sitei140Proton donor; for catalytic activityBy similarity1

GO - Molecular functioni

  • adenosylmethionine decarboxylase activity Source: EcoCyc

GO - Biological processi

  • S-adenosylmethioninamine biosynthetic process Source: UniProtKB-HAMAP
  • spermidine biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Polyamine biosynthesis, Spermidine biosynthesis

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciEcoCyc:SPED-MONOMER.
ECOL316407:JW0116-MONOMER.
MetaCyc:SPED-MONOMER.
SABIO-RKP0A7F6.
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:speD
Ordered Locus Names:b0120, JW0116
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10962. speD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000300431 – 111S-adenosylmethionine decarboxylase beta chainAdd BLAST111
ChainiPRO_0000030044112 – 264S-adenosylmethionine decarboxylase alpha chainAdd BLAST153

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei112Pyruvic acid (Ser); by autocatalysis1

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.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei111 – 112Cleavage (non-hydrolytic); by autolysis2

Keywords - PTMi

Autocatalytic cleavage, Zymogen

Proteomic databases

PaxDbiP0A7F6.
PRIDEiP0A7F6.

Interactioni

Subunit structurei

Heterooctamer of four alpha and four beta chains arranged as a tetramer of alpha/beta heterodimers.1 Publication

Protein-protein interaction databases

BioGridi4262031. 9 interactors.
DIPiDIP-47936N.
IntActiP0A7F6. 4 interactors.
STRINGi511145.b0120.

Structurei

3D structure databases

ProteinModelPortaliP0A7F6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105FDS. Bacteria.
COG1586. LUCA.
HOGENOMiHOG000116821.
InParanoidiP0A7F6.
KOiK01611.
OMAiYNAERLT.

Family and domain databases

Gene3Di3.60.90.10. 1 hit.
HAMAPiMF_00465. AdoMetDC_2. 1 hit.
InterProiIPR003826. AdoMetDC_fam_prok.
IPR009165. S-AdoMet_deCO2ase_bac.
IPR016067. S-AdoMet_deCO2ase_core.
[Graphical view]
PfamiPF02675. AdoMet_dc. 1 hit.
[Graphical view]
PIRSFiPIRSF001356. SAM_decarboxylas. 1 hit.
SUPFAMiSSF56276. SSF56276. 2 hits.
TIGRFAMsiTIGR03331. SAM_DCase_Eco. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P0A7F6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKLKLHGFN NLTKSLSFCI YDICYAKTAE ERDGYIAYID ELYNANRLTE
60 70 80 90 100
ILSETCSIIG ANILNIARQD YEPQGASVTI LVSEEPVDPK LIDKTEHPGP
110 120 130 140 150
LPETVVAHLD KSHICVHTYP ESHPEGGLCT FRADIEVSTC GVISPLKALN
160 170 180 190 200
YLIHQLESDI VTIDYRVRGF TRDINGMKHF IDHEINSIQN FMSDDMKALY
210 220 230 240 250
DMVDVNVYQE NIFHTKMLLK EFDLKHYMFH TKPEDLTDSE RQEITAALWK
260
EMREIYYGRN MPAV
Length:264
Mass (Da):30,385
Last modified:June 7, 2005 - v1
Checksum:iE228BCF8EBDD0325
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02804 Genomic DNA. Translation: AAA24644.1.
U00096 Genomic DNA. Translation: AAC73231.1.
AP009048 Genomic DNA. Translation: BAB96694.1.
PIRiB29778. DCECDM.
RefSeqiNP_414662.1. NC_000913.3.
WP_000734287.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73231; AAC73231; b0120.
BAB96694; BAB96694; BAB96694.
GeneIDi947719.
KEGGiecj:JW0116.
eco:b0120.
PATRICi32115341. VBIEscCol129921_0122.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02804 Genomic DNA. Translation: AAA24644.1.
U00096 Genomic DNA. Translation: AAC73231.1.
AP009048 Genomic DNA. Translation: BAB96694.1.
PIRiB29778. DCECDM.
RefSeqiNP_414662.1. NC_000913.3.
WP_000734287.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0A7F6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262031. 9 interactors.
DIPiDIP-47936N.
IntActiP0A7F6. 4 interactors.
STRINGi511145.b0120.

Proteomic databases

PaxDbiP0A7F6.
PRIDEiP0A7F6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73231; AAC73231; b0120.
BAB96694; BAB96694; BAB96694.
GeneIDi947719.
KEGGiecj:JW0116.
eco:b0120.
PATRICi32115341. VBIEscCol129921_0122.

Organism-specific databases

EchoBASEiEB0955.
EcoGeneiEG10962. speD.

Phylogenomic databases

eggNOGiENOG4105FDS. Bacteria.
COG1586. LUCA.
HOGENOMiHOG000116821.
InParanoidiP0A7F6.
KOiK01611.
OMAiYNAERLT.

Enzyme and pathway databases

UniPathwayiUPA00331; UER00451.
BioCyciEcoCyc:SPED-MONOMER.
ECOL316407:JW0116-MONOMER.
MetaCyc:SPED-MONOMER.
SABIO-RKP0A7F6.

Miscellaneous databases

PROiP0A7F6.

Family and domain databases

Gene3Di3.60.90.10. 1 hit.
HAMAPiMF_00465. AdoMetDC_2. 1 hit.
InterProiIPR003826. AdoMetDC_fam_prok.
IPR009165. S-AdoMet_deCO2ase_bac.
IPR016067. S-AdoMet_deCO2ase_core.
[Graphical view]
PfamiPF02675. AdoMet_dc. 1 hit.
[Graphical view]
PIRSFiPIRSF001356. SAM_decarboxylas. 1 hit.
SUPFAMiSSF56276. SSF56276. 2 hits.
TIGRFAMsiTIGR03331. SAM_DCase_Eco. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSPED_ECOLI
AccessioniPrimary (citable) accession number: P0A7F6
Secondary accession number(s): P09159
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: November 2, 2016
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Spermidine-deficient mutants show a small decrease in growth rate and increased sensibility to superoxide toxicity.

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.