ID L0M4J0_ENTBF Unreviewed; 231 AA.
AC L0M4J0;
DT 06-MAR-2013, integrated into UniProtKB/TrEMBL.
DT 06-MAR-2013, sequence version 1.
DT 27-MAR-2024, entry version 61.
DE RecName: Full=ATP-dependent dethiobiotin synthetase BioD {ECO:0000256|HAMAP-Rule:MF_00336};
DE EC=6.3.3.3 {ECO:0000256|HAMAP-Rule:MF_00336};
DE AltName: Full=DTB synthetase {ECO:0000256|HAMAP-Rule:MF_00336};
DE Short=DTBS {ECO:0000256|HAMAP-Rule:MF_00336};
DE AltName: Full=Dethiobiotin synthase {ECO:0000256|HAMAP-Rule:MF_00336};
GN Name=bioD {ECO:0000256|HAMAP-Rule:MF_00336};
GN OrderedLocusNames=D782_2241 {ECO:0000313|EMBL:AGB78222.1};
OS Enterobacteriaceae bacterium (strain FGI 57).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae.
OX NCBI_TaxID=693444 {ECO:0000313|EMBL:AGB78222.1, ECO:0000313|Proteomes:UP000011002};
RN [1] {ECO:0000313|EMBL:AGB78222.1, ECO:0000313|Proteomes:UP000011002}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FGI 57 {ECO:0000313|EMBL:AGB78222.1,
RC ECO:0000313|Proteomes:UP000011002};
RX PubMed=23469353; DOI=10.1128/genomeA.00238-12;
RA Aylward F.O., Tremmel D.M., Bruce D.C., Chain P., Chen A.,
RA Walston Davenport K., Detter C., Han C.S., Han J., Huntemann M.,
RA Ivanova N.N., Kyrpides N.C., Markowitz V., Mavrommatis K., Nolan M.,
RA Pagani I., Pati A., Pitluck S., Deshpande S., Goodwin L., Woyke T.,
RA Currie C.R.;
RT "Complete genome of Enterobacteriaceae bacterium strain FGI 57, a strain
RT associated with leaf-cutter ant fungus gardens.";
RL Genome Announc. 1:E00238-12(2013).
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:0000256|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:0000256|HAMAP-
CC Rule:MF_00336};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00336};
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
CC diaminononanoate: step 1/2. {ECO:0000256|HAMAP-Rule:MF_00336}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00336}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00336}.
CC -!- SIMILARITY: Belongs to the dethiobiotin synthetase family.
CC {ECO:0000256|HAMAP-Rule:MF_00336}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00336}.
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DR EMBL; CP003938; AGB78222.1; -; Genomic_DNA.
DR AlphaFoldDB; L0M4J0; -.
DR STRING; 693444.D782_2241; -.
DR KEGG; ebf:D782_2241; -.
DR PATRIC; fig|693444.3.peg.2159; -.
DR eggNOG; COG0132; Bacteria.
DR HOGENOM; CLU_072551_0_0_6; -.
DR OrthoDB; 9802097at2; -.
DR UniPathway; UPA00078; UER00161.
DR Proteomes; UP000011002; 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 CDD; cd03109; DTBS; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR HAMAP; MF_00336; BioD; 1.
DR InterPro; IPR004472; DTB_synth_BioD.
DR InterPro; IPR027417; P-loop_NTPase.
DR NCBIfam; TIGR00347; bioD; 1.
DR PANTHER; PTHR43210:SF4; ATP-DEPENDENT DETHIOBIOTIN SYNTHETASE BIOD 2; 1.
DR PANTHER; PTHR43210; DETHIOBIOTIN SYNTHETASE; 1.
DR Pfam; PF13500; AAA_26; 1.
DR PIRSF; PIRSF006755; DTB_synth; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00336};
KW Biotin biosynthesis {ECO:0000256|HAMAP-Rule:MF_00336};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00336};
KW Ligase {ECO:0000256|HAMAP-Rule:MF_00336};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00336};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00336};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00336};
KW Reference proteome {ECO:0000313|Proteomes:UP000011002}.
FT ACT_SITE 38
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 13..18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 17
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 55
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 55
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 112..115
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 112
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 172..173
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 201..203
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
FT BINDING 208
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00336"
SQ SEQUENCE 231 AA; 24878 MW; 5567DA3D3F3C357B CRC64;
MLNRFFITGT DTSVGKTVVS RALLQALAAS GKRVAGYKPV AKGSKETPEG LRNKDALVLQ
SVSSLELPYD AVNPIALSEE KSSVAHSCPI NYTLLSNGLA SLSEKVDNVV VEGTGGWRSL
MNDLRPLSEW VVQEQLPVVM VVGIQEGCIN HALLTAQAIA NDGLPLIGWV ANRINPGLAH
YAEIIDVLSK KLPAPLIGEL PYLPRAEQRE LSQYINLSML SNVLTVDRIL A
//
