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P19623 (SPEE_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 152. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Spermidine synthase

Short name=SPDSY
EC=2.5.1.16
Alternative name(s):
Putrescine aminopropyltransferase
Gene names
Name:SRM
Synonyms:SPS1, SRML1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length302 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.10

Catalytic activity

S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine. Ref.10

Enzyme regulation

The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine. HAMAP-Rule MF_00198

Pathway

Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. HAMAP-Rule MF_00198

Subunit structure

Homodimer or homotetramer. Ref.10

Sequence similarities

Belongs to the spermidine/spermine synthase family.

Contains 1 PABS (polyamine biosynthesis) domain.

Biophysicochemical properties

Kinetic parameters:

KM=20 µM for putrescine Ref.10

KM=0.9 µM for S-adenosylmethioninamine

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 302302Spermidine synthase HAMAP-Rule MF_00198
PRO_0000156445

Regions

Domain18 – 253236PABS
Region155 – 1562S-adenosylmethioninamine binding HAMAP-Rule MF_00198
Region173 – 1764Putrescine binding HAMAP-Rule MF_00198

Sites

Active site1731Proton acceptor By similarity
Binding site491S-adenosylmethioninamine
Binding site791Putrescine
Binding site801S-adenosylmethioninamine
Binding site1041S-adenosylmethioninamine
Binding site1241S-adenosylmethioninamine
Binding site1731S-adenosylmethioninamine
Binding site2411Putrescine

Amino acid modifications

Modified residue11N-acetylmethionine Ref.6 Ref.9

Natural variations

Natural variant1491L → V.
Corresponds to variant rs1049932 [ dbSNP | Ensembl ].
VAR_011807

Experimental info

Sequence conflict2101Q → E in AAA36633. Ref.1

Secondary structure

....................................................... 302
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P19623 [UniParc].

Last modified February 1, 1991. Version 1.
Checksum: 3EF454D886F6425D

FASTA30233,825
        10         20         30         40         50         60 
MEPGPDGPAA SGPAAIREGW FRETCSLWPG QALSLQVEQL LHHRRSRYQD ILVFRSKTYG 

        70         80         90        100        110        120 
NVLVLDGVIQ CTERDEFSYQ EMIANLPLCS HPNPRKVLII GGGDGGVLRE VVKHPSVESV 

       130        140        150        160        170        180 
VQCEIDEDVI QVSKKFLPGM AIGYSSSKLT LHVGDGFEFM KQNQDAFDVI ITDSSDPMGP 

       190        200        210        220        230        240 
AESLFKESYY QLMKTALKED GVLCCQGECQ WLHLDLIKEM RQFCQSLFPV VAYAYCTIPT 

       250        260        270        280        290        300 
YPSGQIGFML CSKNPSTNFQ EPVQPLTQQQ VAQMQLKYYN SDVHRAAFVL PEFARKALND 


VS 

« Hide

References

« Hide 'large scale' references
[1]"Human spermidine synthase: cloning and primary structure."
Wahlfors J., Alhonen L., Kauppinen L., Hyvoenen T., Jaenne J., Eloranta T.
DNA Cell Biol. 9:103-110(1990) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
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]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Structure and mechanism of spermidine synthases."
Wu H., Min J., Ikeguchi Y., Zeng H., Dong A., Loppnau P., Pegg A.E., Plotnikov A.N.
Biochemistry 46:8331-8339(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEXES WITH SPERMIDINE; PUTRESCINE; MTA AND S-ADENOSYLMETHIONINAMINE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS125.1.
PIRA32610.
RefSeqNP_003123.2. NM_003132.2.
UniGeneHs.76244.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP19623.
SMRP19623. Positions 15-299.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112601. 9 interactions.
IntActP19623. 4 interactions.
STRING9606.ENSP00000366156.

Chemistry

BindingDBP19623.
ChEMBLCHEMBL4232.
DrugBankDB00118. S-Adenosylmethionine.
DB00127. Spermine.

PTM databases

PhosphoSiteP19623.

Polymorphism databases

DMDM134811.

Proteomic databases

MaxQBP19623.
PaxDbP19623.
PeptideAtlasP19623.
PRIDEP19623.

Protocols and materials databases

DNASU6723.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000376957; ENSP00000366156; ENSG00000116649.
GeneID6723.
KEGGhsa:6723.
UCSCuc001arz.1. human.

Organism-specific databases

CTD6723.
GeneCardsGC01M011114.
HGNCHGNC:11296. SRM.
HPAHPA015746.
HPA029528.
MIM182891. gene.
neXtProtNX_P19623.
PharmGKBPA36120.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0421.
HOGENOMHOG000256147.
HOVERGENHBG000834.
InParanoidP19623.
KOK00797.
OMAPNVEYAY.
OrthoDBEOG78D7KS.
PhylomeDBP19623.
TreeFamTF314466.

Enzyme and pathway databases

BioCycMetaCyc:HS04027-MONOMER.
ReactomeREACT_111217. Metabolism.
SABIO-RKP19623.
UniPathwayUPA00248; UER00314.

Gene expression databases

ArrayExpressP19623.
BgeeP19623.
CleanExHS_SRM.
GenevestigatorP19623.

Family and domain databases

Gene3D3.40.50.150. 1 hit.
HAMAPMF_00198. Spermidine_synth.
InterProIPR029063. SAM-dependent_MTases-like.
IPR001045. Spermidine/spermine_synthase.
[Graphical view]
PANTHERPTHR11558. PTHR11558. 1 hit.
PfamPF01564. Spermine_synth. 1 hit.
[Graphical view]
SUPFAMSSF53335. SSF53335. 1 hit.
TIGRFAMsTIGR00417. speE. 1 hit.
PROSITEPS01330. PABS_1. 1 hit.
PS51006. PABS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSRM. human.
EvolutionaryTraceP19623.
GenomeRNAi6723.
NextBio26226.
PROP19623.
SOURCESearch...

Entry information

Entry nameSPEE_HUMAN
AccessionPrimary (citable) accession number: P19623
Secondary accession number(s): B1AKP9, Q15511
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1991
Last modified: July 9, 2014
This is version 152 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM