Q9WZC2 (SPEE_THEMA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Spermidine synthase
EC=2.5.1.16

Alternative name(s):
Putrescine aminopropyltransferase
Short name=PAPT
SPDSY

Gene names

Name:	speE
Ordered Locus Names:	TM_0654

Organism

Thermotoga maritima

Taxonomic identifier

2336 [NCBI]

Taxonomic lineage

Bacteria › Thermotogae › Thermotogales › Thermotogaceae › Thermotoga

Protein attributes

Sequence length	296 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor. Has lower affinity and lower activity towards 1,3-diaminopropane, 1,5-diaminopentane, agmatine, thermine and spermidine (in vitro). Ref.2 Ref.3
Catalytic activity	S-adenosylmethioninamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine. Ref.2
Pathway	Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. HAMAP MF_00198
Subunit structure	Homotetramer. Ref.3
Sequence similarities	Belongs to the spermidine/spermine synthase family.
Biophysicochemical properties	Kinetic parameters: KM=20 µM for putrescine Ref.2 Ref.3 KM=0.75 µM for S-adenosylmethioninamine pH dependence: Optimum pH is 7.5. Temperature dependence: Optimum temperature is 90 degrees Celsius.

Ontologies

Keywords
Biological process	Polyamine biosynthesis Spermidine biosynthesis
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	spermidine biosynthetic process Inferred from direct assay Ref.2. Source: UniProtKB
Molecular function	spermidine synthase activity Inferred from direct assay Ref.2. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 296

296

Spermidine synthase HAMAP MF_00198

PRO_0000156513

Regions

Region

152 – 153

2

S-adenosylmethioninamine binding HAMAP MF_00198

Sites

Active site

170

1

Proton acceptor Probable

Binding site

46

1

S-adenosylmethioninamine

Binding site

76

1

Putrescine

Binding site

101

1

S-adenosylmethioninamine

Binding site

121

1

S-adenosylmethioninamine

Binding site

173

1

Putrescine

Binding site

239

1

Putrescine

Experimental info

Mutagenesis

76

1

Y → F: Reduces enzyme activity about 1000-fold. Ref.2

Mutagenesis

101

1

D → I: Reduces enzyme activity over 10000-fold. Ref.2

Mutagenesis

170

1

D → A: Reduces enzyme activity over 10000-fold. Ref.2

Mutagenesis

173

1

D → A: Reduces enzyme activity about 500-fold. Ref.2

Secondary structure

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296

Helix Strand Turn

Details...

Helix

4 – 7

4

Beta strand

15 – 22

8

Beta strand

26 – 33

8

Beta strand

35 – 42

8

Beta strand

47 – 53

7

Turn

54 – 56

3

Beta strand

57 – 62

6

Beta strand

65 – 69

5

Turn

70 – 72

3

Helix

73 – 87

15

Beta strand

88 – 90

3

Beta strand

93 – 98

6

Helix

103 – 108

6

Beta strand

115 – 122

8

Helix

124 – 133

10

Helix

135 – 138

4

Helix

139 – 142

4

Beta strand

146 – 151

6

Helix

153 – 156

4

Helix

157 – 159

3

Beta strand

164 – 170

7

Helix

185 – 194

10

Beta strand

195 – 204

10

Turn

208 – 211

4

Helix

212 – 225

14

Beta strand

227 – 235

9

Beta strand

242 – 252

11

Turn

255 – 258

4

Helix

261 – 265

5

Helix

276 – 281

6

Helix

287 – 292

6

Sequences

	Sequence		Length	Mass (Da)
	Q9WZC2 [UniParc]. Last modified November 1, 1999. Version 1. Checksum: 9298A156B7481945	FASTA	296	34,142
	10 20 30 40 50 60 MRTLKELERE LQPRQHLWYF EYYTGNNVGL FMKMNRVIYS GQSDIQRIDI FENPDLGVVF 70 80 90 100 110 120 ALDGITMTTE KDEFMYHEML AHVPMFLHPN PKKVLIIGGG DGGTLREVLK HDSVEKAILC 130 140 150 160 170 180 EVDGLVIEAA RKYLKQTSCG FDDPRAEIVI ANGAEYVRKF KNEFDVIIID STDPTAGQGG 190 200 210 220 230 240 HLFTEEFYQA CYDALKEDGV FSAETEDPFY DIGWFKLAYR RISKVFPITR VYLGFMTTYP 250 260 270 280 290 SGMWSYTFAS KGIDPIKDFD PEKVRKFNKE LKYYNEEVHV ASFALPNFVK KELGLM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima." Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A., Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M., Cotton M.D., Pratt M.S. , Phillips C.A., Richardson D.L., Heidelberg J.F., Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M. Nature 399:323-329(1999) [PubMed: 10360571] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
[2]	"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: 17585781] [Abstract] Cited for: MUTAGENESIS OF TYR-76; ASP-101; ASP-170 AND ASP-173, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY.
[3]	"The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor." Korolev S., Ikeguchi Y., Skarina T., Beasley S., Arrowsmith C., Edwards A., Joachimiak A., Pegg A.E., Savchenko A. Nat. Struct. Biol. 9:27-31(2002) [PubMed: 11731804] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF APOENZYME AND COMPLEX WITH SUBSTRATE ANALOG, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000512 Genomic DNA. Translation: AAD35738.1.

PIR

C72348.

RefSeq

NP_228463.1. NC_000853.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1INL	X-ray	1.50	A/B/C/D	1-296	[»]
1JQ3	X-ray	1.80	A/B/C/D	1-296	[»]

ProteinModelPortal

Q9WZC2.

SMR

Q9WZC2. Positions 2-296.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

897762.

GenomeReviews

Gene locus TM_0654 in contig AE000512_GR.

KEGG

tma:TM0654.

NMPDR

fig|243274.1.peg.647.

PATRIC

23936222. VBITheMar51294_0664.

TIGR

TM_0654.

Phylogenomic databases

HOGENOM

HBG635113.

OMA

ELWYTEK.

PhylomeDB

Q9WZC2.

ProtClustDB

PRK00811.

Enzyme and pathway databases

BioCyc

TMAR243274:TM_0654-MONOMER.

Family and domain databases

HAMAP

MF_00198. Spermidine_synth.
[Tree]

InterPro

IPR001045. Sprmine_synthase.
[Graphical view]

KO

K00797.

PANTHER

PTHR11558. Sprmine_synthase. 1 hit.

Pfam

PF01564. Spermine_synth. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00417. SpeE. 1 hit.

PROSITE

PS01330. SPERMIDINE_SYNTHASE_1. 1 hit.
PS51006. SPERMIDINE_SYNTHASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SPEE_THEMA

Accession

Primary (citable) accession number: Q9WZC2

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	November 1, 1999
Last modified:	January 25, 2012
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program