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P52788 (SPSY_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 134. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Spermine synthase

Short name=SPMSY
EC=2.5.1.22
Alternative name(s):
Spermidine aminopropyltransferase
Gene names
Name:SMS
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length366 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).

Catalytic activity

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

Pathway

Amine and polyamine biosynthesis; spermine biosynthesis; spermine from spermidine: step 1/1.

Subunit structure

Homodimer. Dimerization is mediated through the N-terminal domain and seems to be required for activity as deletion of the N-terminal domain causes complete loss of activity. Ref.13

Domain

Composed of 3 domains: the N-terminal domain has structural similarity to S-adenosylmethionine decarboxylase, the central domain is made up of four beta strands and the C-terminal domain is similar in structure to spermidine synthase. The N- and C-terminal domains are both required for activity.

Involvement in disease

X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583]: Characterized by moderate intellectual deficit, hypotonia, an unsteady gait, osteoporosis, kyphoscoliosis and facial asymmetry. Transmission is X-linked recessive.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9

Sequence similarities

Belongs to the spermidine/spermine synthase family.

Contains 1 PABS (polyamine biosynthesis) domain.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P52788-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P52788-2)

The sequence of this isoform differs from the canonical sequence as follows:
     57-109: Missing.
Note: Gene prediction confirmed by EST data.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.11
Chain2 – 366365Spermine synthase
PRO_0000156538

Regions

Domain122 – 362241PABS
Region255 – 2562S-adenosylmethioninamine binding

Sites

Active site2761Proton acceptor By similarity
Binding site1481S-adenosylmethioninamine
Binding site1771Spermidine
Binding site2011Spermidine
Binding site2201S-adenosylmethioninamine
Binding site3511Spermidine
Binding site3531Spermidine

Amino acid modifications

Modified residue21N-acetylalanine Ref.11

Natural variations

Alternative sequence57 – 10953Missing in isoform 2.
VSP_034406
Natural variant601N → S. Ref.14
VAR_071048

Experimental info

Mutagenesis2011D → A or N: 100,000-fold decrease in catalytic efficiency. Ref.13
Mutagenesis2761D → N: 200,000-fold decrease in catalytic efficiency. Ref.13
Mutagenesis3531E → Q: 800-fold decrease in catalytic efficiency. Ref.13
Sequence conflict11M → MPG in CAA88921. Ref.1

Secondary structure

............................................................ 366
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: D5B23EF61DE66443

FASTA36641,268
        10         20         30         40         50         60 
MAAARHSTLD FMLGAKADGE TILKGLQSIF QEQGMAESVH TWQDHGYLAT YTNKNGSFAN 

        70         80         90        100        110        120 
LRIYPHGLVL LDLQSYDGDA QGKEEIDSIL NKVEERMKEL SQDSTGRVKR LPPIVRGGAI 

       130        140        150        160        170        180 
DRYWPTADGR LVEYDIDEVV YDEDSPYQNI KILHSKQFGN ILILSGDVNL AESDLAYTRA 

       190        200        210        220        230        240 
IMGSGKEDYT GKDVLILGGG DGGILCEIVK LKPKMVTMVE IDQMVIDGCK KYMRKTCGDV 

       250        260        270        280        290        300 
LDNLKGDCYQ VLIEDCIPVL KRYAKEGREF DYVINDLTAV PISTSPEEDS TWEFLRLILD 

       310        320        330        340        350        360 
LSMKVLKQDG KYFTQGNCVN LTEALSLYEE QLGRLYCPVE FSKEIVCVPS YLELWVFYTV 


WKKAKP 

« Hide

Isoform 2 [UniParc].

Checksum: 7D237FC4CD55D3E6
Show »

FASTA31335,278

References

« Hide 'large scale' references
[1]"Molecular cloning of a cDNA encoding human spermine synthase."
Korhonen V.-P., Halmekytoe M., Kauppinen L., Myoehaenen S., Wahlfors J., Keinaenen T., Hyvoenen T., Alhonen L., Eloranta T., Jaenne J.
DNA Cell Biol. 14:841-847(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"Sequence analysis of 139 kb in Xp22.1 containing spermine synthase and the 5' region of PEX."
Grieff M., Whyte M.P., Thakker R.V., Mazzarella R.
Genomics 44:227-231(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Colon.
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[4]"The DNA sequence of the human X chromosome."
Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. expand/collapse author list , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]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].
[6]"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] (ISOFORM 1).
Tissue: Kidney and Skin.
[7]Eloranta T., Kajander O., Kauppinen L., Hyvoenen T., Linnala-Kankkunen A., Kalkkinen N., Kulomaa M., Alhonen L., Jaenne J.
(In) Goldemberg S.H., Algranati I.D. (eds.); Proceedings of the international symposium on the biology and chemistry of polyamines, pp.91-98, ICSU Press, New York (1988)
Cited for: PARTIAL PROTEIN SEQUENCE.
[8]"Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides."
Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J.
Nat. Biotechnol. 21:566-569(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 97-107 (ISOFORM 1).
Tissue: Platelet.
[9]"X-linked spermine synthase gene (SMS) defect: the first polyamine deficiency syndrome."
Cason A.L., Ikeguchi Y., Skinner C., Wood T.C., Holden K.R., Lubs H.A., Martinez F., Simensen R.J., Stevenson R.E., Pegg A.E., Schwartz C.E.
Eur. J. Hum. Genet. 11:937-944(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN MRXSSR.
[10]"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells."
Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J.
Nat. Biotechnol. 23:94-101(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"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 ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[12]"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].
[13]"Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism."
Wu H., Min J., Zeng H., McCloskey D.E., Ikeguchi Y., Loppnau P., Michael A.J., Pegg A.E., Plotnikov A.N.
J. Biol. Chem. 283:16135-16146(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 5-366 (ISOFORM 1) IN COMPLEX WITH SPERMIDINE AND 5-METHYLTHIOADENOSINE, SUBUNIT, MUTAGENESIS OF ASP-201; ASP-276 AND GLU-353.
[14]"De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability."
UK10K Consortium
Grozeva D., Carss K., Spasic-Boskovic O., Parker M.J., Archer H., Firth H.V., Park S.M., Canham N., Holder S.E., Wilson M., Hackett A., Field M., Floyd J.A., Hurles M., Raymond F.L.
Am. J. Hum. Genet. 94:618-624(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT SER-60.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z49099 mRNA. Translation: CAA88921.1.
AD001528 mRNA. Translation: AAB61308.1.
AK313834 mRNA. Translation: BAG36567.1.
U53331 Genomic DNA. Translation: AAD08634.1.
U73023 Genomic DNA. No translation available.
CH471074 Genomic DNA. Translation: EAW98984.1.
BC009898 mRNA. Translation: AAH09898.1.
BC085621 mRNA. Translation: AAH85621.1.
CCDSCCDS14203.1. [P52788-1]
CCDS59161.1. [P52788-2]
PIRS54160.
RefSeqNP_001245352.1. NM_001258423.1. [P52788-2]
NP_004586.2. NM_004595.4. [P52788-1]
UniGeneHs.724874.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3C6KX-ray1.95A/B/C/D5-366[»]
3C6MX-ray2.45A/B/C/D5-366[»]
ProteinModelPortalP52788.
SMRP52788. Positions 3-365.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112495. 28 interactions.
IntActP52788. 6 interactions.
MINTMINT-5002620.
STRING9606.ENSP00000385746.

Chemistry

BindingDBP52788.
ChEMBLCHEMBL4934.
DrugBankDB00127. Spermine.

PTM databases

PhosphoSiteP52788.

Polymorphism databases

DMDM8247960.

2D gel databases

OGPP52788.

Proteomic databases

MaxQBP52788.
PaxDbP52788.
PRIDEP52788.

Protocols and materials databases

DNASU6611.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000379404; ENSP00000368714; ENSG00000102172. [P52788-2]
ENST00000404933; ENSP00000385746; ENSG00000102172. [P52788-1]
GeneID6611.
KEGGhsa:6611.
UCSCuc004dag.4. human. [P52788-1]
uc031tgx.1. human. [P52788-2]

Organism-specific databases

CTD6611.
GeneCardsGC0XP021958.
GeneReviewsSMS.
HGNCHGNC:11123. SMS.
HPAHPA029849.
HPA029852.
MIM300105. gene.
309583. phenotype.
neXtProtNX_P52788.
Orphanet3063. intellectual disability, X-linked, Snyder type.
PharmGKBPA35972.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG259013.
HOGENOMHOG000007053.
HOVERGENHBG004512.
InParanoidP52788.
KOK00802.
OMAEGRMFDY.
OrthoDBEOG7G1V6F.
PhylomeDBP52788.
TreeFamTF324508.

Enzyme and pathway databases

BioCycMetaCyc:HS02362-MONOMER.
ReactomeREACT_111217. Metabolism.
SABIO-RKP52788.
UniPathwayUPA00249; UER00315.

Gene expression databases

BgeeP52788.
CleanExHS_SMS.
GenevestigatorP52788.

Family and domain databases

Gene3D3.40.50.150. 1 hit.
InterProIPR029063. SAM-dependent_MTases-like.
IPR001045. Spermidine/spermine_synthase.
IPR015576. Spermine_synthase_animal.
[Graphical view]
PANTHERPTHR11558. PTHR11558. 1 hit.
PTHR11558:SF27. PTHR11558:SF27. 1 hit.
PfamPF01564. Spermine_synth. 1 hit.
[Graphical view]
SUPFAMSSF53335. SSF53335. 1 hit.
PROSITEPS01330. PABS_1. 1 hit.
PS51006. PABS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP52788.
GeneWikiSMS_(gene).
GenomeRNAi6611.
NextBio25739.
PROP52788.
SOURCESearch...

Entry information

Entry nameSPSY_HUMAN
AccessionPrimary (citable) accession number: P52788
Secondary accession number(s): A6NHA7 expand/collapse secondary AC list , A6NI34, B2R9M0, O00544, Q9UQS1
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: May 30, 2000
Last modified: July 9, 2014
This is version 134 of the entry and version 2 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 X

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