BIOD_FRATT
ID BIOD_FRATT Reviewed; 225 AA.
AC Q5NGB5;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 94.
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=FTT_0934c;
OS Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales;
OC Francisellaceae; Francisella.
OX NCBI_TaxID=177416;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SCHU S4 / Schu 4;
RX PubMed=15640799; DOI=10.1038/ng1499;
RA Larsson P., Oyston P.C.F., Chain P., Chu M.C., Duffield M., Fuxelius H.-H.,
RA Garcia E., Haelltorp G., Johansson D., Isherwood K.E., Karp P.D.,
RA Larsson E., Liu Y., Michell S., Prior J., Prior R., Malfatti S.,
RA Sjoestedt A., Svensson K., Thompson N., Vergez L., Wagg J.K., Wren B.W.,
RA Lindler L.E., Andersson S.G.E., Forsman M., Titball R.W.;
RT "The complete genome sequence of Francisella tularensis, the causative
RT agent of tularemia.";
RL Nat. Genet. 37:153-159(2005).
RN [2] {ECO:0007744|PDB:3OF5}
RP X-RAY CRYSTALLOGRAPHY (1.52 ANGSTROMS), AND SUBUNIT.
RC STRAIN=SCHU S4 / Schu 4;
RA Brunzelle J.S., Skarina T., Gordon E., Savchenko A., Anderson W.F.;
RT "Crystal structure of a dethiobiotin synthetase from Francisella tularensis
RT subsp. tularensis SCHU S4.";
RL Submitted (AUG-2010) to the PDB data bank.
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 ECO:0000269|Ref.2}.
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; AJ749949; CAG45567.1; -; Genomic_DNA.
DR RefSeq; WP_003020969.1; NZ_CP010290.1.
DR RefSeq; YP_169927.1; NC_006570.2.
DR PDB; 3OF5; X-ray; 1.52 A; A/B=1-225.
DR PDBsum; 3OF5; -.
DR AlphaFoldDB; Q5NGB5; -.
DR SMR; Q5NGB5; -.
DR STRING; 177416.FTT_0934c; -.
DR DNASU; 3190963; -.
DR EnsemblBacteria; CAG45567; CAG45567; FTT_0934c.
DR KEGG; ftu:FTT_0934c; -.
DR eggNOG; COG0132; Bacteria.
DR OMA; SPHWAAE; -.
DR UniPathway; UPA00078; UER00161.
DR EvolutionaryTrace; Q5NGB5; -.
DR Proteomes; UP000001174; 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; ISS:UniProtKB.
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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Biotin biosynthesis; Cytoplasm; Ligase;
KW Magnesium; Metal-binding; Nucleotide-binding; Reference proteome.
FT CHAIN 1..225
FT /note="ATP-dependent dethiobiotin synthetase BioD"
FT /id="PRO_0000302508"
FT ACT_SITE 37
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 41
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 52
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 52
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 114..117
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 114
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 174..175
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT STRAND 2..13
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 15..28
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 51..59
FT /evidence="ECO:0007829|PDB:3OF5"
FT TURN 60..62
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 66..69
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 80..86
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 93..101
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 102..105
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 109..118
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 129..136
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 140..145
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 150..163
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 168..175
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 183..194
FT /evidence="ECO:0007829|PDB:3OF5"
FT STRAND 199..205
FT /evidence="ECO:0007829|PDB:3OF5"
FT HELIX 208..218
FT /evidence="ECO:0007829|PDB:3OF5"
SQ SEQUENCE 225 AA; 25189 MW; 30D1D017AAAC89AC CRC64;
MKKFFIIGTD TEVGKTYIST KLIEVCEHQN IKSLCLKPVA SGQSQFSELC EDVESILNAY
KHKFTAAEIN LISFNQAVAP HIIAAKTKVD ISIENLKQFI EDKYNQDLDI LFIEGAGGLL
TPYSDHTTQL DLIKALQIPV LLVSAIKVGC INHTLLTINE LNRHNIKLAG WIANCNDSNI
KYIDEQINTI EELSGYKCSA KISRNADYLD FIDLSKILIS PEENE
