BIOD_SPHAL
ID BIOD_SPHAL Reviewed; 202 AA.
AC Q1GT35;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 27-JUN-2006, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=ATP-dependent dethiobiotin synthetase BioD {ECO:0000255|HAMAP-Rule:MF_00336};
DE EC=6.3.3.3 {ECO:0000255|HAMAP-Rule:MF_00336};
DE AltName: Full=DTB synthetase {ECO:0000255|HAMAP-Rule:MF_00336};
DE Short=DTBS {ECO:0000255|HAMAP-Rule:MF_00336};
DE AltName: Full=Dethiobiotin synthase {ECO:0000255|HAMAP-Rule:MF_00336};
GN Name=bioD {ECO:0000255|HAMAP-Rule:MF_00336}; OrderedLocusNames=Sala_1474;
OS Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256)
OS (Sphingomonas alaskensis).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingopyxis.
OX NCBI_TaxID=317655;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 13593 / LMG 18877 / RB2256;
RX PubMed=19805210; DOI=10.1073/pnas.0903507106;
RA Lauro F.M., McDougald D., Thomas T., Williams T.J., Egan S., Rice S.,
RA DeMaere M.Z., Ting L., Ertan H., Johnson J., Ferriera S., Lapidus A.,
RA Anderson I., Kyrpides N., Munk A.C., Detter C., Han C.S., Brown M.V.,
RA Robb F.T., Kjelleberg S., Cavicchioli R.;
RT "The genomic basis of trophic strategy in marine bacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:15527-15533(2009).
CC -!- FUNCTION: Catalyzes a mechanistically unusual reaction, the ATP-
CC dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-
CC diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to
CC form a ureido ring. {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(7R,8S)-7,8-diammoniononanoate + ATP + CO2 = (4R,5S)-
CC dethiobiotin + ADP + 3 H(+) + phosphate; Xref=Rhea:RHEA:15805,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:149469, ChEBI:CHEBI:149473,
CC ChEBI:CHEBI:456216; EC=6.3.3.3; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00336};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00336};
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
CC diaminononanoate: step 1/2. {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- SIMILARITY: Belongs to the dethiobiotin synthetase family.
CC {ECO:0000255|HAMAP-Rule:MF_00336}.
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DR EMBL; CP000356; ABF53187.1; -; Genomic_DNA.
DR RefSeq; WP_011541767.1; NC_008048.1.
DR AlphaFoldDB; Q1GT35; -.
DR SMR; Q1GT35; -.
DR STRING; 317655.Sala_1474; -.
DR EnsemblBacteria; ABF53187; ABF53187; Sala_1474.
DR KEGG; sal:Sala_1474; -.
DR eggNOG; COG0132; Bacteria.
DR HOGENOM; CLU_072551_2_0_5; -.
DR OMA; SPHWAAE; -.
DR OrthoDB; 1739932at2; -.
DR UniPathway; UPA00078; UER00161.
DR Proteomes; UP000006578; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004141; F:dethiobiotin synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009102; P:biotin biosynthetic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00336; BioD; 1.
DR InterPro; IPR004472; DTB_synth_BioD.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR43210; PTHR43210; 1.
DR PIRSF; PIRSF006755; DTB_synth; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00347; bioD; 1.
PE 3: Inferred from homology;
KW ATP-binding; Biotin biosynthesis; Cytoplasm; Ligase; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome.
FT CHAIN 1..202
FT /note="ATP-dependent dethiobiotin synthetase BioD"
FT /id="PRO_1000059711"
FT ACT_SITE 32
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 12..17
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 16
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 36
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 43
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 43
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 94..97
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 94
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 178..180
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ SEQUENCE 202 AA; 21507 MW; 6747C389422C5B50 CRC64;
MTRFVVTGTD TGIGKTIFSA SLARATGTPY WKPVQSGLEE ETDSEIVARL AGVPVRPEAY
RLVTPASPHI AAEIDGVAID IERLTPPPGE LIVEGAGGAL VPVTRRTLYA ELFARWQVPV
IVCARTSLGT INHSLLTIEA LKRRDVPIHG VVFIGDAVED SEAIIADVSG VRRLGRLPVV
APLTSENLAA AFGANFDIAD FR
