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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

    Pathwayi: spermidine 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)DescriptionActionsGraphical viewLength
    Binding sitei49S-adenosylmethioninamine1
    Binding sitei79Putrescine1
    Binding sitei80S-adenosylmethioninamine1
    Binding sitei104S-adenosylmethioninamine1
    Binding sitei124S-adenosylmethioninamine1
    Active sitei173Proton acceptorBy similarity1
    Binding sitei173S-adenosylmethioninamine1
    Binding sitei241Putrescine1

    GO - Molecular functioni

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

    GO - Biological processi

    • polyamine metabolic process Source: Reactome
    • spermidine biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Polyamine biosynthesis, Spermidine biosynthesis

    Enzyme and pathway databases

    BioCyciMetaCyc:HS04027-MONOMER.
    ZFISH:HS04027-MONOMER.
    BRENDAi2.5.1.16. 2681.
    ReactomeiR-HSA-351202. 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
    Proteomesi
    • UP000005640 Componenti: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:11296. SRM.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Organism-specific databases

    DisGeNETi6723.
    OpenTargetsiENSG00000116649.
    PharmGKBiPA36120.

    Chemistry databases

    ChEMBLiCHEMBL4232.
    DrugBankiDB00118. S-Adenosylmethionine.

    Polymorphism and mutation databases

    BioMutaiSRM.
    DMDMi134811.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001564451 – 302Spermidine synthaseAdd BLAST302

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei1N-acetylmethionineCombined sources1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    EPDiP19623.
    MaxQBiP19623.
    PaxDbiP19623.
    PeptideAtlasiP19623.
    PRIDEiP19623.

    PTM databases

    iPTMnetiP19623.
    PhosphoSitePlusiP19623.

    Expressioni

    Gene expression databases

    BgeeiENSG00000116649.
    CleanExiHS_SRM.
    ExpressionAtlasiP19623. baseline and differential.
    GenevisibleiP19623. HS.

    Organism-specific databases

    HPAiHPA015746.
    HPA029528.

    Interactioni

    Subunit structurei

    Homodimer or homotetramer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-1056183,EBI-1056183
    TERF1P542742EBI-1056183,EBI-710997

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Protein-protein interaction databases

    BioGridi112601. 20 interactors.
    IntActiP19623. 7 interactors.
    STRINGi9606.ENSP00000366156.

    Chemistry databases

    BindingDBiP19623.

    Structurei

    Secondary structure

    1302
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi20 – 23Combined sources4
    Beta strandi31 – 45Combined sources15
    Beta strandi47 – 59Combined sources13
    Beta strandi61 – 65Combined sources5
    Beta strandi68 – 72Combined sources5
    Turni73 – 76Combined sources4
    Helixi77 – 88Combined sources12
    Beta strandi91 – 93Combined sources3
    Beta strandi96 – 101Combined sources6
    Helixi106 – 111Combined sources6
    Beta strandi119 – 125Combined sources7
    Helixi127 – 136Combined sources10
    Helixi138 – 141Combined sources4
    Helixi142 – 145Combined sources4
    Beta strandi149 – 154Combined sources6
    Helixi156 – 161Combined sources6
    Beta strandi167 – 173Combined sources7
    Helixi179 – 185Combined sources7
    Helixi188 – 196Combined sources9
    Beta strandi197 – 208Combined sources12
    Turni210 – 212Combined sources3
    Helixi214 – 227Combined sources14
    Beta strandi229 – 237Combined sources9
    Helixi242 – 244Combined sources3
    Beta strandi245 – 254Combined sources10
    Beta strandi259 – 261Combined sources3
    Helixi268 – 273Combined sources6
    Helixi281 – 286Combined sources6
    Helixi292 – 299Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP19623.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini18 – 253PABSAdd BLAST236

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni155 – 156S-adenosylmethioninamine binding2
    Regioni173 – 176Putrescine binding4

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG1562. Eukaryota.
    COG0421. LUCA.
    GeneTreeiENSGT00860000133776.
    HOGENOMiHOG000256147.
    HOVERGENiHBG000834.
    InParanoidiP19623.
    KOiK00797.
    OMAiLEAYCTT.
    OrthoDBiEOG091G07LZ.
    PhylomeDBiP19623.
    TreeFamiTF314466.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    HAMAPiMF_00198. Spermidine_synth. 1 hit.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti210Q → E in AAA36633 (PubMed:2344393).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_011807149L → V.Corresponds to variant rs1049932dbSNPEnsembl.1

    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.2. 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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi112601. 20 interactors.
    IntActiP19623. 7 interactors.
    STRINGi9606.ENSP00000366156.

    Chemistry databases

    BindingDBiP19623.
    ChEMBLiCHEMBL4232.
    DrugBankiDB00118. S-Adenosylmethionine.

    PTM databases

    iPTMnetiP19623.
    PhosphoSitePlusiP19623.

    Polymorphism and mutation databases

    BioMutaiSRM.
    DMDMi134811.

    Proteomic databases

    EPDiP19623.
    MaxQBiP19623.
    PaxDbiP19623.
    PeptideAtlasiP19623.
    PRIDEiP19623.

    Protocols and materials databases

    DNASUi6723.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000376957; ENSP00000366156; ENSG00000116649.
    GeneIDi6723.
    KEGGihsa:6723.
    UCSCiuc001arz.2. human.

    Organism-specific databases

    CTDi6723.
    DisGeNETi6723.
    GeneCardsiSRM.
    HGNCiHGNC:11296. SRM.
    HPAiHPA015746.
    HPA029528.
    MIMi182891. gene.
    neXtProtiNX_P19623.
    OpenTargetsiENSG00000116649.
    PharmGKBiPA36120.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG1562. Eukaryota.
    COG0421. LUCA.
    GeneTreeiENSGT00860000133776.
    HOGENOMiHOG000256147.
    HOVERGENiHBG000834.
    InParanoidiP19623.
    KOiK00797.
    OMAiLEAYCTT.
    OrthoDBiEOG091G07LZ.
    PhylomeDBiP19623.
    TreeFamiTF314466.

    Enzyme and pathway databases

    UniPathwayiUPA00248; UER00314.
    BioCyciMetaCyc:HS04027-MONOMER.
    ZFISH:HS04027-MONOMER.
    BRENDAi2.5.1.16. 2681.
    ReactomeiR-HSA-351202. Metabolism of polyamines.
    SABIO-RKP19623.

    Miscellaneous databases

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

    Gene expression databases

    BgeeiENSG00000116649.
    CleanExiHS_SRM.
    ExpressionAtlasiP19623. baseline and differential.
    GenevisibleiP19623. HS.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    HAMAPiMF_00198. Spermidine_synth. 1 hit.
    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...

    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: November 30, 2016
    This is version 175 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

    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.