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Protein

Spermidine synthase

Gene

SRM

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM). Has a strong preference for putrescine as substrate, and has very low activity towards 1,3-diaminopropane. Has extremely low activity towards spermidine.1 Publication

Catalytic activityi

S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine.1 Publication

Enzyme regulationi

The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine.

Kineticsi

  1. KM=20 µM for putrescine1 Publication
  2. KM=0.9 µM for S-adenosylmethioninamine1 Publication

    Pathway:ispermidine biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes spermidine from putrescine.
    Proteins known to be involved in this subpathway in this organism are:
    1. Spermidine synthase (SRM)
    This subpathway is part of the pathway spermidine 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 spermidine from putrescine, the pathway spermidine biosynthesis and in Amine and polyamine biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei49 – 491S-adenosylmethioninamine
    Binding sitei79 – 791Putrescine
    Binding sitei80 – 801S-adenosylmethioninamine
    Binding sitei104 – 1041S-adenosylmethioninamine
    Binding sitei124 – 1241S-adenosylmethioninamine
    Active sitei173 – 1731Proton acceptorBy similarity
    Binding sitei173 – 1731S-adenosylmethioninamine
    Binding sitei241 – 2411Putrescine

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB
    • spermidine synthase activity Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Polyamine biosynthesis, Spermidine biosynthesis

    Enzyme and pathway databases

    BioCyciMetaCyc:HS04027-MONOMER.
    BRENDAi2.5.1.16. 2681.
    ReactomeiREACT_14820. Metabolism of polyamines.
    SABIO-RKP19623.
    UniPathwayiUPA00248; UER00314.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Spermidine synthase (EC:2.5.1.16)
    Short name:
    SPDSY
    Alternative name(s):
    Putrescine aminopropyltransferase
    Gene namesi
    Name:SRM
    Synonyms:SPS1, SRML1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640 Componenti: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:11296. SRM.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA36120.

    Chemistry

    DrugBankiDB00118. S-Adenosylmethionine.

    Polymorphism and mutation databases

    BioMutaiSRM.
    DMDMi134811.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 302302Spermidine synthasePRO_0000156445Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine2 Publications

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP19623.
    PaxDbiP19623.
    PeptideAtlasiP19623.
    PRIDEiP19623.

    PTM databases

    PhosphoSiteiP19623.

    Expressioni

    Gene expression databases

    BgeeiP19623.
    CleanExiHS_SRM.
    ExpressionAtlasiP19623. baseline and differential.
    GenevisibleiP19623. HS.

    Organism-specific databases

    HPAiHPA015746.
    HPA029528.

    Interactioni

    Subunit structurei

    Homodimer or homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi112601. 10 interactions.
    IntActiP19623. 4 interactions.
    STRINGi9606.ENSP00000366156.

    Structurei

    Secondary structure

    1
    302
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi20 – 234Combined sources
    Beta strandi31 – 4515Combined sources
    Beta strandi47 – 5913Combined sources
    Beta strandi61 – 655Combined sources
    Beta strandi68 – 725Combined sources
    Turni73 – 764Combined sources
    Helixi77 – 8812Combined sources
    Beta strandi91 – 933Combined sources
    Beta strandi96 – 1016Combined sources
    Helixi106 – 1116Combined sources
    Beta strandi119 – 1257Combined sources
    Helixi127 – 13610Combined sources
    Helixi138 – 1414Combined sources
    Helixi142 – 1454Combined sources
    Beta strandi149 – 1546Combined sources
    Helixi156 – 1616Combined sources
    Beta strandi167 – 1737Combined sources
    Helixi179 – 1857Combined sources
    Helixi188 – 1969Combined sources
    Beta strandi197 – 20812Combined sources
    Turni210 – 2123Combined sources
    Helixi214 – 22714Combined sources
    Beta strandi229 – 2379Combined sources
    Helixi242 – 2443Combined sources
    Beta strandi245 – 25410Combined sources
    Beta strandi259 – 2613Combined sources
    Helixi268 – 2736Combined sources
    Helixi281 – 2866Combined sources
    Helixi292 – 2998Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O05X-ray2.00A/B1-302[»]
    2O06X-ray2.00A/B1-302[»]
    2O07X-ray1.89A/B1-302[»]
    2O0LX-ray1.99A/B1-302[»]
    3RW9X-ray2.00A/B1-302[»]
    ProteinModelPortaliP19623.
    SMRiP19623. Positions 15-299.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP19623.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini18 – 253236PABSAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni155 – 1562S-adenosylmethioninamine binding
    Regioni173 – 1764Putrescine binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0421.
    GeneTreeiENSGT00620000088039.
    HOGENOMiHOG000256147.
    HOVERGENiHBG000834.
    InParanoidiP19623.
    KOiK00797.
    OMAiVEEAWLC.
    OrthoDBiEOG78D7KS.
    PhylomeDBiP19623.
    TreeFamiTF314466.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    HAMAPiMF_00198. Spermidine_synth.
    InterProiIPR030374. PABS.
    IPR030373. PABS_CS.
    IPR029063. SAM-dependent_MTases.
    IPR001045. Spermi_synthase.
    IPR030668. Spermi_synthase_euk.
    [Graphical view]
    PIRSFiPIRSF000502. Spermidine_synth. 1 hit.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00417. speE. 1 hit.
    PROSITEiPS01330. PABS_1. 1 hit.
    PS51006. PABS_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P19623-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEPGPDGPAA SGPAAIREGW FRETCSLWPG QALSLQVEQL LHHRRSRYQD
    60 70 80 90 100
    ILVFRSKTYG NVLVLDGVIQ CTERDEFSYQ EMIANLPLCS HPNPRKVLII
    110 120 130 140 150
    GGGDGGVLRE VVKHPSVESV VQCEIDEDVI QVSKKFLPGM AIGYSSSKLT
    160 170 180 190 200
    LHVGDGFEFM KQNQDAFDVI ITDSSDPMGP AESLFKESYY QLMKTALKED
    210 220 230 240 250
    GVLCCQGECQ WLHLDLIKEM RQFCQSLFPV VAYAYCTIPT YPSGQIGFML
    260 270 280 290 300
    CSKNPSTNFQ EPVQPLTQQQ VAQMQLKYYN SDVHRAAFVL PEFARKALND

    VS
    Length:302
    Mass (Da):33,825
    Last modified:February 1, 1991 - v1
    Checksum:i3EF454D886F6425D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti210 – 2101Q → E in AAA36633 (PubMed:2344393).Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti149 – 1491L → V.
    Corresponds to variant rs1049932 [ dbSNP | Ensembl ].
    VAR_011807

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M34338 mRNA. Translation: AAA36633.1.
    M64231 Genomic DNA. Translation: AAA60574.1.
    AL109811 Genomic DNA. Translation: CAI22104.1.
    CH471130 Genomic DNA. Translation: EAW71675.1.
    BC000309 mRNA. Translation: AAH00309.1.
    BC033106 mRNA. Translation: AAH33106.1.
    CCDSiCCDS125.1.
    PIRiA32610.
    RefSeqiNP_003123.2. NM_003132.2.
    UniGeneiHs.76244.

    Genome annotation databases

    EnsembliENST00000376957; ENSP00000366156; ENSG00000116649.
    GeneIDi6723.
    KEGGihsa:6723.
    UCSCiuc001arz.1. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M34338 mRNA. Translation: AAA36633.1.
    M64231 Genomic DNA. Translation: AAA60574.1.
    AL109811 Genomic DNA. Translation: CAI22104.1.
    CH471130 Genomic DNA. Translation: EAW71675.1.
    BC000309 mRNA. Translation: AAH00309.1.
    BC033106 mRNA. Translation: AAH33106.1.
    CCDSiCCDS125.1.
    PIRiA32610.
    RefSeqiNP_003123.2. NM_003132.2.
    UniGeneiHs.76244.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O05X-ray2.00A/B1-302[»]
    2O06X-ray2.00A/B1-302[»]
    2O07X-ray1.89A/B1-302[»]
    2O0LX-ray1.99A/B1-302[»]
    3RW9X-ray2.00A/B1-302[»]
    ProteinModelPortaliP19623.
    SMRiP19623. Positions 15-299.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi112601. 10 interactions.
    IntActiP19623. 4 interactions.
    STRINGi9606.ENSP00000366156.

    Chemistry

    BindingDBiP19623.
    ChEMBLiCHEMBL4232.
    DrugBankiDB00118. S-Adenosylmethionine.

    PTM databases

    PhosphoSiteiP19623.

    Polymorphism and mutation databases

    BioMutaiSRM.
    DMDMi134811.

    Proteomic databases

    MaxQBiP19623.
    PaxDbiP19623.
    PeptideAtlasiP19623.
    PRIDEiP19623.

    Protocols and materials databases

    DNASUi6723.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000376957; ENSP00000366156; ENSG00000116649.
    GeneIDi6723.
    KEGGihsa:6723.
    UCSCiuc001arz.1. human.

    Organism-specific databases

    CTDi6723.
    GeneCardsiGC01M011114.
    HGNCiHGNC:11296. SRM.
    HPAiHPA015746.
    HPA029528.
    MIMi182891. gene.
    neXtProtiNX_P19623.
    PharmGKBiPA36120.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiCOG0421.
    GeneTreeiENSGT00620000088039.
    HOGENOMiHOG000256147.
    HOVERGENiHBG000834.
    InParanoidiP19623.
    KOiK00797.
    OMAiVEEAWLC.
    OrthoDBiEOG78D7KS.
    PhylomeDBiP19623.
    TreeFamiTF314466.

    Enzyme and pathway databases

    UniPathwayiUPA00248; UER00314.
    BioCyciMetaCyc:HS04027-MONOMER.
    BRENDAi2.5.1.16. 2681.
    ReactomeiREACT_14820. Metabolism of polyamines.
    SABIO-RKP19623.

    Miscellaneous databases

    ChiTaRSiSRM. human.
    EvolutionaryTraceiP19623.
    GenomeRNAii6723.
    NextBioi26226.
    PROiP19623.
    SOURCEiSearch...

    Gene expression databases

    BgeeiP19623.
    CleanExiHS_SRM.
    ExpressionAtlasiP19623. baseline and differential.
    GenevisibleiP19623. HS.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    HAMAPiMF_00198. Spermidine_synth.
    InterProiIPR030374. PABS.
    IPR030373. PABS_CS.
    IPR029063. SAM-dependent_MTases.
    IPR001045. Spermi_synthase.
    IPR030668. Spermi_synthase_euk.
    [Graphical view]
    PIRSFiPIRSF000502. Spermidine_synth. 1 hit.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00417. speE. 1 hit.
    PROSITEiPS01330. PABS_1. 1 hit.
    PS51006. PABS_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Human spermidine synthase gene: structure and chromosomal localization."
      Myoehaenen S., Kauppinen L., Wahlfors J., Alhonen L., Jaenne J.
      DNA Cell Biol. 10:467-474(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "The DNA sequence and biological annotation of human chromosome 1."
      Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
      , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
      Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Lung and Skin.
    6. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
      Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
      Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEXES WITH SPERMIDINE; PUTRESCINE; MTA AND S-ADENOSYLMETHIONINAMINE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

    Entry informationi

    Entry nameiSPEE_HUMAN
    AccessioniPrimary (citable) accession number: P19623
    Secondary accession number(s): B1AKP9, Q15511
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1991
    Last sequence update: February 1, 1991
    Last modified: July 22, 2015
    This is version 162 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 1
      Human chromosome 1: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    6. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    7. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.