SELD_ECOLI
ID SELD_ECOLI Reviewed; 347 AA.
AC P16456; P78172;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=Selenide, water dikinase {ECO:0000255|HAMAP-Rule:MF_00625};
DE EC=2.7.9.3 {ECO:0000255|HAMAP-Rule:MF_00625, ECO:0000269|PubMed:22081394, ECO:0000269|PubMed:2405383};
DE AltName: Full=Selenium donor protein {ECO:0000255|HAMAP-Rule:MF_00625};
DE AltName: Full=Selenophosphate synthase {ECO:0000255|HAMAP-Rule:MF_00625};
GN Name=selD {ECO:0000255|HAMAP-Rule:MF_00625}; Synonyms=fdhB;
GN OrderedLocusNames=b1764, JW1753;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=2405383; DOI=10.1073/pnas.87.2.543;
RA Leinfelder W., Forchhammer K., Veprek B., Zehelein E., Boeck A.;
RT "In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA):
RT involvement and characterization of the selD gene product.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:543-547(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 236-347.
RC STRAIN=HMS-83;
RX PubMed=2553698; DOI=10.1016/s0021-9258(19)84661-6;
RA Digate R.J., Marians K.J.;
RT "Molecular cloning and DNA sequence analysis of Escherichia coli topB, the
RT gene encoding topoisomerase III.";
RL J. Biol. Chem. 264:17924-17930(1989).
RN [6]
RP MUTAGENESIS OF CYS-17 AND CYS-19.
RX PubMed=1527085; DOI=10.1016/s0021-9258(18)41824-8;
RA Kim I.Y., Veres Z., Stadtman T.C.;
RT "Escherichia coli mutant SELD enzymes. The cysteine 17 residue is essential
RT for selenophosphate formation from ATP and selenide.";
RL J. Biol. Chem. 267:19650-19654(1992).
RN [7]
RP MUTAGENESIS OF HIS-13; GLY-18 AND LYS-20.
RX PubMed=8262938; DOI=10.1016/s0021-9258(19)74212-4;
RA Kim I.Y., Veres Z., Stadtman T.C.;
RT "Biochemical analysis of Escherichia coli selenophosphate synthetase
RT mutants. Lysine 20 is essential for catalytic activity and cysteine 17/19
RT for 8-azido-ATP derivatization.";
RL J. Biol. Chem. 268:27020-27025(1993).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF MUTANT SER-17 IN COMPLEX WITH
RP MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND MUTAGENESIS OF
RP ASP-51; ASP-68; ASN-87; ASP-91 AND ASP-227.
RX PubMed=22081394; DOI=10.1128/jb.06012-11;
RA Noinaj N., Wattanasak R., Lee D.Y., Wally J.L., Piszczek G., Chock P.B.,
RA Stadtman T.C., Buchanan S.K.;
RT "Structural insights into the catalytic mechanism of Escherichia coli
RT selenophosphate synthetase.";
RL J. Bacteriol. 194:499-508(2012).
CC -!- FUNCTION: Synthesizes selenophosphate from selenide and ATP.
CC {ECO:0000255|HAMAP-Rule:MF_00625, ECO:0000269|PubMed:22081394,
CC ECO:0000269|PubMed:2405383}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O + hydrogenselenide = AMP + 2 H(+) + phosphate +
CC selenophosphate; Xref=Rhea:RHEA:18737, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16144, ChEBI:CHEBI:29317,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456215; EC=2.7.9.3;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00625,
CC ECO:0000269|PubMed:22081394, ECO:0000269|PubMed:2405383};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00625,
CC ECO:0000269|PubMed:22081394};
CC Note=Binds 1 Mg(2+) ion per monomer. {ECO:0000255|HAMAP-Rule:MF_00625,
CC ECO:0000269|PubMed:22081394};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00625,
CC ECO:0000269|PubMed:22081394}.
CC -!- SIMILARITY: Belongs to the selenophosphate synthase 1 family. Class I
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00625, ECO:0000305}.
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DR EMBL; M30184; AAA74748.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74834.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15552.1; -; Genomic_DNA.
DR EMBL; J05076; AAA83922.1; -; Genomic_DNA.
DR PIR; JW0033; JW0033.
DR RefSeq; NP_416278.1; NC_000913.3.
DR RefSeq; WP_001295485.1; NZ_SSZK01000001.1.
DR PDB; 3U0O; X-ray; 2.25 A; A/B=1-347.
DR PDBsum; 3U0O; -.
DR AlphaFoldDB; P16456; -.
DR SMR; P16456; -.
DR BioGRID; 4259138; 21.
DR DIP; DIP-10849N; -.
DR IntAct; P16456; 11.
DR STRING; 511145.b1764; -.
DR jPOST; P16456; -.
DR PaxDb; P16456; -.
DR PRIDE; P16456; -.
DR DNASU; 946768; -.
DR EnsemblBacteria; AAC74834; AAC74834; b1764.
DR EnsemblBacteria; BAA15552; BAA15552; BAA15552.
DR GeneID; 60900049; -.
DR GeneID; 946768; -.
DR KEGG; ecj:JW1753; -.
DR KEGG; eco:b1764; -.
DR PATRIC; fig|1411691.4.peg.490; -.
DR EchoBASE; EB0936; -.
DR eggNOG; COG0709; Bacteria.
DR InParanoid; P16456; -.
DR OMA; DNEPKYG; -.
DR PhylomeDB; P16456; -.
DR BioCyc; EcoCyc:EG10943-MON; -.
DR BioCyc; MetaCyc:EG10943-MON; -.
DR BRENDA; 2.7.9.3; 2026.
DR PRO; PR:P16456; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0004756; F:selenide, water dikinase activity; IDA:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0016260; P:selenocysteine biosynthetic process; IDA:UniProtKB.
DR GO; GO:0070329; P:tRNA seleno-modification; IMP:EcoCyc.
DR CDD; cd02195; SelD; 1.
DR Gene3D; 3.30.1330.10; -; 1.
DR Gene3D; 3.90.650.10; -; 1.
DR HAMAP; MF_00625; SelD; 1.
DR InterPro; IPR010918; PurM-like_C_dom.
DR InterPro; IPR036676; PurM-like_C_sf.
DR InterPro; IPR016188; PurM-like_N.
DR InterPro; IPR036921; PurM-like_N_sf.
DR InterPro; IPR023061; SelD_I.
DR InterPro; IPR004536; SPS/SelD.
DR PANTHER; PTHR10256; PTHR10256; 1.
DR Pfam; PF00586; AIRS; 1.
DR Pfam; PF02769; AIRS_C; 1.
DR PIRSF; PIRSF036407; Selenphspht_syn; 1.
DR SUPFAM; SSF55326; SSF55326; 1.
DR SUPFAM; SSF56042; SSF56042; 1.
DR TIGRFAMs; TIGR00476; selD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Selenium; Transferase.
FT CHAIN 1..347
FT /note="Selenide, water dikinase"
FT /id="PRO_0000127620"
FT ACT_SITE 17
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00625"
FT BINDING 20
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903, ECO:0000255|HAMAP-
FT Rule:MF_00625"
FT BINDING 48..50
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903, ECO:0000255|HAMAP-
FT Rule:MF_00625"
FT BINDING 51
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00625,
FT ECO:0000269|PubMed:22081394, ECO:0007744|PDB:3U0O"
FT BINDING 68
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903, ECO:0000255|HAMAP-
FT Rule:MF_00625"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903, ECO:0000255|HAMAP-
FT Rule:MF_00625"
FT BINDING 91
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00625,
FT ECO:0000269|PubMed:22081394, ECO:0007744|PDB:3U0O"
FT BINDING 139..141
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P49903, ECO:0000255|HAMAP-
FT Rule:MF_00625"
FT BINDING 227
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00625,
FT ECO:0000269|PubMed:22081394, ECO:0007744|PDB:3U0O"
FT SITE 20
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00625,
FT ECO:0000269|PubMed:8262938"
FT MUTAGEN 13
FT /note="H->N: No loss of activity."
FT /evidence="ECO:0000269|PubMed:8262938"
FT MUTAGEN 17
FT /note="C->S: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:1527085,
FT ECO:0000269|PubMed:22081394"
FT MUTAGEN 18
FT /note="G->V: Partial loss of activity."
FT /evidence="ECO:0000269|PubMed:8262938"
FT MUTAGEN 19
FT /note="C->S: No loss of activity."
FT /evidence="ECO:0000269|PubMed:1527085"
FT MUTAGEN 20
FT /note="K->Q: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:8262938"
FT MUTAGEN 20
FT /note="K->R: Marked loss of activity."
FT /evidence="ECO:0000269|PubMed:8262938"
FT MUTAGEN 51
FT /note="D->A: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:22081394"
FT MUTAGEN 68
FT /note="D->A: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:22081394"
FT MUTAGEN 87
FT /note="N->A: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:22081394"
FT MUTAGEN 91
FT /note="D->A: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:22081394"
FT MUTAGEN 227
FT /note="D->A: Complete loss of activity."
FT /evidence="ECO:0000269|PubMed:22081394"
FT STRAND 22..27
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 60..71
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 77..94
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 98..108
FT /evidence="ECO:0007829|PDB:3U0O"
FT TURN 110..112
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 115..131
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 136..143
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 148..158
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 173..178
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 182..190
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 201..207
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 212..216
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 222..227
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 232..244
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 246..251
FT /evidence="ECO:0007829|PDB:3U0O"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 261..265
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 272..281
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 290..296
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 305..309
FT /evidence="ECO:0007829|PDB:3U0O"
FT HELIX 311..323
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 332..336
FT /evidence="ECO:0007829|PDB:3U0O"
FT STRAND 341..345
FT /evidence="ECO:0007829|PDB:3U0O"
SQ SEQUENCE 347 AA; 36687 MW; 595E5EC9F7B1370F CRC64;
MSENSIRLTQ YSHGAGCGCK ISPKVLETIL HSEQAKFVDP NLLVGNETRD DAAVYDLGNG
TSVISTTDFF MPIVDNPFDF GRIAATNAIS DIFAMGGKPI MAIAILGWPI NKLSPEIARE
VTEGGRYACR QAGIALAGGH SIDAPEPIFG LAVTGIVPTE RVKKNSTAQA GCKLFLTKPL
GIGVLTTAEK KSLLKPEHQG LATEVMCRMN IAGASFANIE GVKAMTDVTG FGLLGHLSEM
CQGAGVQARV DYEAIPKLPG VEEYIKLGAV PGGTERNFAS YGHLMGEMPR EVRDLLCDPQ
TSGGLLLAVM PEAENEVKAT AAEFGIELTA IGELVPARGG RAMVEIR
