BIOD_CROS5
ID BIOD_CROS5 Reviewed; 221 AA.
AC B1WZW5;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 20-MAY-2008, sequence version 1.
DT 03-AUG-2022, entry version 77.
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=cce_3516;
OS Crocosphaera subtropica (strain ATCC 51142 / BH68) (Cyanothece sp. (strain
OS ATCC 51142)).
OC Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales;
OC Aphanothecaceae; Crocosphaera; Crocosphaera subtropica.
OX NCBI_TaxID=43989;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51142 / BH68;
RX PubMed=18812508; DOI=10.1073/pnas.0805418105;
RA Welsh E.A., Liberton M., Stoeckel J., Loh T., Elvitigala T., Wang C.,
RA Wollam A., Fulton R.S., Clifton S.W., Jacobs J.M., Aurora R., Ghosh B.K.,
RA Sherman L.A., Smith R.D., Wilson R.K., Pakrasi H.B.;
RT "The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium
RT important in the marine nitrogen cycle.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:15094-15099(2008).
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 (By similarity). This cyanobacterium does not encode
CC bioA (which catalyzes the formation of the precursor for this reaction
CC in the cannonical pathway), instead it encodes bioU, which replaces
CC bioA and also performs the first half of the cannonical BioD reaction.
CC Thus in this organism BioD has a different substrate (By similarity).
CC {ECO:0000250|UniProtKB:Q55849, 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 -!- CATALYTIC ACTIVITY:
CC Reaction=(7R,8S)-8-amino-7-(carboxyamino)nonanoate + ATP = (4R,5S)-
CC dethiobiotin + ADP + H(+) + phosphate; Xref=Rhea:RHEA:63684,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:149470, ChEBI:CHEBI:149473, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000250|UniProtKB:Q55849, ECO:0000305};
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; CP000806; ACB52864.1; -; Genomic_DNA.
DR RefSeq; WP_009545318.1; NC_010546.1.
DR AlphaFoldDB; B1WZW5; -.
DR SMR; B1WZW5; -.
DR STRING; 43989.cce_3516; -.
DR EnsemblBacteria; ACB52864; ACB52864; cce_3516.
DR KEGG; cyt:cce_3516; -.
DR eggNOG; COG0132; Bacteria.
DR HOGENOM; CLU_072551_3_1_3; -.
DR OMA; KMLLISH; -.
DR OrthoDB; 1739932at2; -.
DR UniPathway; UPA00078; UER00161.
DR Proteomes; UP000001203; Chromosome circular.
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..221
FT /note="ATP-dependent dethiobiotin synthetase BioD"
FT /id="PRO_1000133212"
FT ACT_SITE 39
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 43
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 47
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 47
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 105..108
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 105
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 165..166
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ SEQUENCE 221 AA; 24103 MW; 1E07CE911A4480B7 CRC64;
MTTLFIVGTD TEVGKTVVTS ALAAYWQTYH SSESLGVIKL LQTGIGDVEH YQRLLPHVEV
VNPLRYETPV APPVAAEKEN RSIPLDQVWQ GLNDLQQRKN LVLAEGLGGL GSPVTWELTV
ADLAGEWGLP TVLVVPVKLG AIAQTVANVA LARQYKVNLK GIIFSCPRPL SHEEIVNFAP
ITLIESLTKT PVLGMISYLE NIEDITKLAH IASSLDLEML F
