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Protein

Selenide, water dikinase

Gene

selD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Synthesizes selenophosphate from selenide and ATP.

Catalytic activityi

ATP + selenide + H2O = AMP + selenophosphate + phosphate.

Cofactori

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei17 – 171Sequence analysis
Sitei20 – 201Important for catalytic activity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi230 – 2367ATPSequence analysis

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • magnesium ion binding Source: EcoCyc
  • selenide, water dikinase activity Source: EcoCyc

GO - Biological processi

  • selenocysteine biosynthetic process Source: EcoCyc
  • tRNA seleno-modification Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, Magnesium, Nucleotide-binding, Selenium

Enzyme and pathway databases

BioCyciEcoCyc:EG10943-MONOMER.
ECOL316407:JW1753-MONOMER.
MetaCyc:EG10943-MONOMER.
BRENDAi2.7.9.3. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Selenide, water dikinase (EC:2.7.9.3)
Alternative name(s):
Selenium donor protein
Selenophosphate synthase
Gene namesi
Name:selD
Synonyms:fdhB
Ordered Locus Names:b1764, JW1753
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10943. selD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi13 – 131H → N: No loss of activity. 1 Publication
Mutagenesisi17 – 171C → S: Complete loss of activity. 1 Publication
Mutagenesisi18 – 181G → V: Partial loss of activity. 1 Publication
Mutagenesisi19 – 191C → S: No loss of activity. 1 Publication
Mutagenesisi20 – 201K → Q: Complete loss of activity. 1 Publication
Mutagenesisi20 – 201K → R: Marked loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 347347Selenide, water dikinasePRO_0000127620Add
BLAST

Proteomic databases

EPDiP16456.
PaxDbiP16456.
PRIDEiP16456.

Interactioni

Subunit structurei

Monomer.Curated

Protein-protein interaction databases

BioGridi4259138. 16 interactions.
DIPiDIP-10849N.
IntActiP16456. 11 interactions.
MINTiMINT-1256873.
STRINGi511145.b1764.

Structurei

Secondary structure

1
347
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi22 – 276Combined sources
Beta strandi41 – 433Combined sources
Beta strandi51 – 566Combined sources
Beta strandi60 – 7112Combined sources
Helixi77 – 9418Combined sources
Beta strandi98 – 10811Combined sources
Turni110 – 1123Combined sources
Helixi115 – 13117Combined sources
Beta strandi136 – 1438Combined sources
Beta strandi148 – 15811Combined sources
Helixi159 – 1613Combined sources
Beta strandi173 – 1786Combined sources
Helixi182 – 1909Combined sources
Helixi196 – 1983Combined sources
Helixi201 – 2077Combined sources
Helixi212 – 2165Combined sources
Beta strandi222 – 2276Combined sources
Helixi232 – 24413Combined sources
Beta strandi246 – 2516Combined sources
Turni252 – 2543Combined sources
Helixi261 – 2655Combined sources
Helixi272 – 28110Combined sources
Helixi282 – 2843Combined sources
Helixi290 – 2967Combined sources
Beta strandi305 – 3095Combined sources
Helixi311 – 32313Combined sources
Beta strandi332 – 3365Combined sources
Beta strandi341 – 3455Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3U0OX-ray2.25A/B1-347[»]
ProteinModelPortaliP16456.
SMRiP16456. Positions 13-347.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105D4F. Bacteria.
COG0709. LUCA.
HOGENOMiHOG000219300.
InParanoidiP16456.
KOiK01008.
OMAiPGSRFGK.
OrthoDBiEOG6VF32H.
PhylomeDBiP16456.

Family and domain databases

Gene3Di3.30.1330.10. 1 hit.
3.90.650.10. 1 hit.
HAMAPiMF_00625. SelD.
InterProiIPR010918. AIR_synth_C_dom.
IPR016188. PurM-like_N.
IPR023061. SelD_I.
IPR004536. SPS/SelD.
[Graphical view]
PfamiPF00586. AIRS. 1 hit.
PF02769. AIRS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF036407. Selenphspht_syn. 1 hit.
SUPFAMiSSF56042. SSF56042. 1 hit.
TIGRFAMsiTIGR00476. selD. 1 hit.

Sequencei

Sequence statusi: Complete.

P16456-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSENSIRLTQ YSHGAGCGCK ISPKVLETIL HSEQAKFVDP NLLVGNETRD
60 70 80 90 100
DAAVYDLGNG TSVISTTDFF MPIVDNPFDF GRIAATNAIS DIFAMGGKPI
110 120 130 140 150
MAIAILGWPI NKLSPEIARE VTEGGRYACR QAGIALAGGH SIDAPEPIFG
160 170 180 190 200
LAVTGIVPTE RVKKNSTAQA GCKLFLTKPL GIGVLTTAEK KSLLKPEHQG
210 220 230 240 250
LATEVMCRMN IAGASFANIE GVKAMTDVTG FGLLGHLSEM CQGAGVQARV
260 270 280 290 300
DYEAIPKLPG VEEYIKLGAV PGGTERNFAS YGHLMGEMPR EVRDLLCDPQ
310 320 330 340
TSGGLLLAVM PEAENEVKAT AAEFGIELTA IGELVPARGG RAMVEIR
Length:347
Mass (Da):36,687
Last modified:August 1, 1990 - v1
Checksum:i595E5EC9F7B1370F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30184 Genomic DNA. Translation: AAA74748.1.
U00096 Genomic DNA. Translation: AAC74834.1.
AP009048 Genomic DNA. Translation: BAA15552.1.
J05076 Genomic DNA. Translation: AAA83922.1.
PIRiJW0033.
RefSeqiNP_416278.1. NC_000913.3.
WP_001295485.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74834; AAC74834; b1764.
BAA15552; BAA15552; BAA15552.
GeneIDi946768.
KEGGiecj:JW1753.
eco:b1764.
PATRICi32118839. VBIEscCol129921_1837.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30184 Genomic DNA. Translation: AAA74748.1.
U00096 Genomic DNA. Translation: AAC74834.1.
AP009048 Genomic DNA. Translation: BAA15552.1.
J05076 Genomic DNA. Translation: AAA83922.1.
PIRiJW0033.
RefSeqiNP_416278.1. NC_000913.3.
WP_001295485.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3U0OX-ray2.25A/B1-347[»]
ProteinModelPortaliP16456.
SMRiP16456. Positions 13-347.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259138. 16 interactions.
DIPiDIP-10849N.
IntActiP16456. 11 interactions.
MINTiMINT-1256873.
STRINGi511145.b1764.

Proteomic databases

EPDiP16456.
PaxDbiP16456.
PRIDEiP16456.

Protocols and materials databases

DNASUi946768.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74834; AAC74834; b1764.
BAA15552; BAA15552; BAA15552.
GeneIDi946768.
KEGGiecj:JW1753.
eco:b1764.
PATRICi32118839. VBIEscCol129921_1837.

Organism-specific databases

EchoBASEiEB0936.
EcoGeneiEG10943. selD.

Phylogenomic databases

eggNOGiENOG4105D4F. Bacteria.
COG0709. LUCA.
HOGENOMiHOG000219300.
InParanoidiP16456.
KOiK01008.
OMAiPGSRFGK.
OrthoDBiEOG6VF32H.
PhylomeDBiP16456.

Enzyme and pathway databases

BioCyciEcoCyc:EG10943-MONOMER.
ECOL316407:JW1753-MONOMER.
MetaCyc:EG10943-MONOMER.
BRENDAi2.7.9.3. 2026.

Miscellaneous databases

PROiP16456.

Family and domain databases

Gene3Di3.30.1330.10. 1 hit.
3.90.650.10. 1 hit.
HAMAPiMF_00625. SelD.
InterProiIPR010918. AIR_synth_C_dom.
IPR016188. PurM-like_N.
IPR023061. SelD_I.
IPR004536. SPS/SelD.
[Graphical view]
PfamiPF00586. AIRS. 1 hit.
PF02769. AIRS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF036407. Selenphspht_syn. 1 hit.
SUPFAMiSSF56042. SSF56042. 1 hit.
TIGRFAMsiTIGR00476. selD. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product."
    Leinfelder W., Forchhammer K., Veprek B., Zehelein E., Boeck A.
    Proc. Natl. Acad. Sci. U.S.A. 87:543-547(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III."
    Digate R.J., Marians K.J.
    J. Biol. Chem. 264:17924-17930(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 236-347.
    Strain: HMS-83.
  6. "Escherichia coli mutant SELD enzymes. The cysteine 17 residue is essential for selenophosphate formation from ATP and selenide."
    Kim I.Y., Veres Z., Stadtman T.C.
    J. Biol. Chem. 267:19650-19654(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-17 AND CYS-19.
  7. "Biochemical analysis of Escherichia coli selenophosphate synthetase mutants. Lysine 20 is essential for catalytic activity and cysteine 17/19 for 8-azido-ATP derivatization."
    Kim I.Y., Veres Z., Stadtman T.C.
    J. Biol. Chem. 268:27020-27025(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS.

Entry informationi

Entry nameiSELD_ECOLI
AccessioniPrimary (citable) accession number: P16456
Secondary accession number(s): P78172
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: April 13, 2016
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.