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P19623

- SPEE_HUMAN

UniProt

P19623 - SPEE_HUMAN

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Protein

Spermidine synthase

Gene

SRM

Organism
Homo sapiens (Human)
Status
Reviewed - 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

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

  1. protein homodimerization activity Source: UniProtKB
  2. spermidine synthase activity Source: UniProtKB

GO - Biological processi

  1. cellular nitrogen compound metabolic process Source: Reactome
  2. polyamine metabolic process Source: Reactome
  3. small molecule metabolic process Source: Reactome
  4. 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.
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: Chromosome 1

Organism-specific databases

HGNCiHGNC:11296. SRM.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: Reactome
Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA36120.

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.
GenevestigatoriP19623.

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
Turni177 – 1793Combined sources
Helixi180 – 1856Combined 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.
OMAiPNVEYAY.
OrthoDBiEOG78D7KS.
PhylomeDBiP19623.
TreeFamiTF314466.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_00198. Spermidine_synth.
InterProiIPR029063. SAM-dependent_MTases-like.
IPR001045. Spermidine/spermine_synthase.
[Graphical view]
PANTHERiPTHR11558. PTHR11558. 1 hit.
PfamiPF01564. Spermine_synth. 1 hit.
[Graphical view]
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.

Polymorphism databases

DMDMi134811.

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 .
CCDSi CCDS125.1.
PIRi A32610.
RefSeqi NP_003123.2. NM_003132.2.
UniGenei Hs.76244.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2O05 X-ray 2.00 A/B 1-302 [» ]
2O06 X-ray 2.00 A/B 1-302 [» ]
2O07 X-ray 1.89 A/B 1-302 [» ]
2O0L X-ray 1.99 A/B 1-302 [» ]
3RW9 X-ray 2.00 A/B 1-302 [» ]
ProteinModelPortali P19623.
SMRi P19623. Positions 15-299.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 112601. 10 interactions.
IntActi P19623. 4 interactions.
STRINGi 9606.ENSP00000366156.

Chemistry

BindingDBi P19623.
ChEMBLi CHEMBL4232.
DrugBanki DB00118. S-Adenosylmethionine.

PTM databases

PhosphoSitei P19623.

Polymorphism databases

DMDMi 134811.

Proteomic databases

MaxQBi P19623.
PaxDbi P19623.
PeptideAtlasi P19623.
PRIDEi P19623.

Protocols and materials databases

DNASUi 6723.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000376957 ; ENSP00000366156 ; ENSG00000116649 .
GeneIDi 6723.
KEGGi hsa:6723.
UCSCi uc001arz.1. human.

Organism-specific databases

CTDi 6723.
GeneCardsi GC01M011114.
HGNCi HGNC:11296. SRM.
HPAi HPA015746.
HPA029528.
MIMi 182891. gene.
neXtProti NX_P19623.
PharmGKBi PA36120.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0421.
GeneTreei ENSGT00620000088039.
HOGENOMi HOG000256147.
HOVERGENi HBG000834.
InParanoidi P19623.
KOi K00797.
OMAi PNVEYAY.
OrthoDBi EOG78D7KS.
PhylomeDBi P19623.
TreeFami TF314466.

Enzyme and pathway databases

UniPathwayi UPA00248 ; UER00314 .
BioCyci MetaCyc:HS04027-MONOMER.
Reactomei REACT_14820. Metabolism of polyamines.
SABIO-RK P19623.

Miscellaneous databases

ChiTaRSi SRM. human.
EvolutionaryTracei P19623.
GenomeRNAii 6723.
NextBioi 26226.
PROi P19623.
SOURCEi Search...

Gene expression databases

Bgeei P19623.
CleanExi HS_SRM.
ExpressionAtlasi P19623. baseline and differential.
Genevestigatori P19623.

Family and domain databases

Gene3Di 3.40.50.150. 1 hit.
HAMAPi MF_00198. Spermidine_synth.
InterProi IPR029063. SAM-dependent_MTases-like.
IPR001045. Spermidine/spermine_synthase.
[Graphical view ]
PANTHERi PTHR11558. PTHR11558. 1 hit.
Pfami PF01564. Spermine_synth. 1 hit.
[Graphical view ]
SUPFAMi SSF53335. SSF53335. 1 hit.
TIGRFAMsi TIGR00417. speE. 1 hit.
PROSITEi PS01330. PABS_1. 1 hit.
PS51006. PABS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: November 26, 2014
This is version 156 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