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Database: UniProt
Entry: BIOD_CLOK1
LinkDB: BIOD_CLOK1
Original site: BIOD_CLOK1 
ID   BIOD_CLOK1              Reviewed;         241 AA.
AC   B9E076;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   24-MAR-2009, sequence version 1.
DT   27-MAR-2024, entry version 75.
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=CKR_0850;
OS   Clostridium kluyveri (strain NBRC 12016).
OC   Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae;
OC   Clostridium.
OX   NCBI_TaxID=583346;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=NBRC 12016;
RA   Inui M., Nonaka H., Shinoda Y., Ikenaga Y., Abe M., Naito K., Vertes A.A.,
RA   Yukawa H.;
RT   "Complete genome sequence of Clostridium kluyveri and comparative genomics
RT   of Clostridia species.";
RL   Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
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; AP009049; BAH05901.1; -; Genomic_DNA.
DR   RefSeq; WP_012101317.1; NC_011837.1.
DR   AlphaFoldDB; B9E076; -.
DR   SMR; B9E076; -.
DR   KEGG; ckr:CKR_0850; -.
DR   HOGENOM; CLU_072551_3_0_9; -.
DR   UniPathway; UPA00078; UER00161.
DR   Proteomes; UP000007969; 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:SF2; 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; Biotin biosynthesis; Cytoplasm; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding.
FT   CHAIN           1..241
FT                   /note="ATP-dependent dethiobiotin synthetase BioD"
FT                   /id="PRO_1000133211"
FT   ACT_SITE        38
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         13..18
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         17
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         42
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         55
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         55
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         116..119
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         116
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         180..181
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ   SEQUENCE   241 AA;  26750 MW;  00A907DC6105CC49 CRC64;
     MAKGIFIVGT DTDIGKTVVT AGLMHVLRSR GYNAVYFKAA LSGALEIDNK LIPSDTKLVS
     DVSKLEEPYE NITPYVYRTG VSPHLAARLE NNPMDLDIVK EKYVYLKEKY DFIIAEGSGG
     IVCPLIDDGR GVYTIGNLIK DLNMSVIIVA SAGLGTINHT VLTAKYIENL GIKIEGIIIN
     KYEKDLFYDD NIGMIEKITK LPIVAKLKNI KDMNDNEIEA IRIHSEKAFS AENIIKHMEQ
     L
//
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