Selenide, water dikinase - Escherichia coli (strain K12)

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P16456 (SELD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 113. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Selenide, water dikinase
EC=2.7.9.3

Alternative name(s):
Selenium donor protein
Selenophosphate synthase

Gene names

Name:	selD
Synonyms:	fdhB
Ordered Locus Names:	b1764, JW1753

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	347 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Synthesizes selenophosphate from selenide and ATP. HAMAP-Rule MF_00625
Catalytic activity	ATP + selenide + H₂O = AMP + selenophosphate + phosphate. HAMAP-Rule MF_00625
Cofactor	Magnesium.
Subunit structure	Monomer Potential.
Sequence similarities	Belongs to the selenophosphate synthase 1 family. Class I subfamily.

Ontologies

Keywords
Ligand	ATP-binding Magnesium Nucleotide-binding Selenium
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	selenocysteine biosynthetic process Inferred from mutant phenotype Ref.1 PubMed 2962989. Source: EcoCyc tRNA seleno-modification Inferred from mutant phenotype Ref.1 PubMed 2962989. Source: EcoCyc
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from direct assay PubMed 22081394. Source: EcoCyc selenide, water dikinase activity Inferred from direct assay PubMed 1606960. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 347

347

Selenide, water dikinase HAMAP-Rule MF_00625

PRO_0000127620

Regions

Nucleotide binding

230 – 236

ATP Potential

Sites

Active site

Potential

Site

Important for catalytic activity

Experimental info

Mutagenesis

H → N: No loss of activity.

Mutagenesis

C → S: Complete loss of activity. Ref.6

Mutagenesis

G → V: Partial loss of activity.

Mutagenesis

C → S: No loss of activity. Ref.6

Mutagenesis

K → Q: Complete loss of activity.

Mutagenesis

K → R: Marked loss of activity.

Secondary structure

347

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P16456 [UniParc].

Last modified August 1, 1990. Version 1.
Checksum: 595E5EC9F7B1370F
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FASTA

347

36,687

        10         20         30         40         50         60 
MSENSIRLTQ YSHGAGCGCK ISPKVLETIL HSEQAKFVDP NLLVGNETRD DAAVYDLGNG 

        70         80         90        100        110        120 
TSVISTTDFF MPIVDNPFDF GRIAATNAIS DIFAMGGKPI MAIAILGWPI NKLSPEIARE 

       130        140        150        160        170        180 
VTEGGRYACR QAGIALAGGH SIDAPEPIFG LAVTGIVPTE RVKKNSTAQA GCKLFLTKPL 

       190        200        210        220        230        240 
GIGVLTTAEK KSLLKPEHQG LATEVMCRMN IAGASFANIE GVKAMTDVTG FGLLGHLSEM 

       250        260        270        280        290        300 
CQGAGVQARV DYEAIPKLPG VEEYIKLGAV PGGTERNFAS YGHLMGEMPR EVRDLLCDPQ 

       310        320        330        340 
TSGGLLLAVM PEAENEVKAT AAEFGIELTA IGELVPARGG RAMVEIR

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. Horiuchi T. DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M30184 Genomic DNA. Translation: AAA74748.1.
U00096 Genomic DNA. Translation: AAC74834.1.
AP009048 Genomic DNA. Translation: BAA15552.1.
J05076 Genomic DNA. Translation: AAA83922.1.

PIR

JW0033.

RefSeq

NP_416278.1. NC_000913.2.
YP_490025.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3U0O	X-ray	2.25	A/B	1-347	[»]

ProteinModelPortal

P16456.

SMR

P16456. Positions 13-347.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10849N.

IntAct

P16456. 11 interactions.

MINT

MINT-1256873.

STRING

511145.b1764.

Proteomic databases

PaxDb

P16456.

PRIDE

P16456.

Protocols and materials databases

DNASU

946768.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74834; AAC74834; b1764.
BAA15552; BAA15552; BAA15552.

GeneID

12930144.
946768.

KEGG

ecj:Y75_p1739.
eco:b1764.

PATRIC

32118839. VBIEscCol129921_1837.

Organism-specific databases

EchoBASE

EB0936.

EcoGene

EG10943. selD.

Phylogenomic databases

eggNOG

COG0709.

HOGENOM

HOG000219300.

K01008.

OMA

PIRLTQY.

ProtClustDB

PRK00943.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10943-MONOMER.
ECOL316407:JW1753-MONOMER.
MetaCyc:EG10943-MONOMER.

Gene expression databases

Genevestigator

P16456.

Family and domain databases

HAMAP

MF_00625. SelD.

InterPro

IPR010918. AIR_synth_C_dom.
IPR000728. AIR_synth_N_dom.
IPR016188. PurM_N-like.
IPR004536. SelD.
IPR023061. SelD_I.
[Graphical view]

Pfam

PF00586. AIRS. 1 hit.
PF02769. AIRS_C. 1 hit.
[Graphical view]

PIRSF

PIRSF036407. Selenphspht_syn. 1 hit.

SUPFAM

SSF56042. AIR_synth_C. 1 hit.
SSF55326. PurM_N-like. 1 hit.

TIGRFAMs

TIGR00476. selD. 1 hit.

ProtoNet

Search...

Entry information

Entry name

SELD_ECOLI

Accession

Primary (citable) accession number: P16456
Secondary accession number(s): P78172

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	August 1, 1990
Last modified:	May 1, 2013
This is version 113 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents