ID BIOD_HELPY Reviewed; 218 AA. AC O24872; DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot. DT 01-JAN-1998, sequence version 1. DT 27-MAR-2024, entry version 134. 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}; GN OrderedLocusNames=HP_0029; OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori). OC Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; OC Helicobacteraceae; Helicobacter. OX NCBI_TaxID=85962; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 700392 / 26695; RX PubMed=9252185; DOI=10.1038/41483; RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A., RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.; RT "The complete genome sequence of the gastric pathogen Helicobacter RT pylori."; RL Nature 388:539-547(1997). RN [2] {ECO:0007744|PDB:2QMO, ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS, ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0} RP X-RAY CRYSTALLOGRAPHY (1.34 ANGSTROMS) IN COMPLEX WITH NUCLEOTIDES; RP SUBSTRATE ANALOG; PHOSPHATE PRODUCT AND MAGNESIUM, PROBABLE ACTIVE SITE, RP COFACTOR, SUBUNIT, AND DOMAIN. RX PubMed=22284390; DOI=10.1111/j.1742-4658.2012.08506.x; RA Porebski P.J., Klimecka M., Chruszcz M., Nicholls R.A., Murzyn K., RA Cuff M.E., Xu X., Cymborowski M., Murshudov G.N., Savchenko A., Edwards A., RA Minor W.; RT "Structural characterization of Helicobacter pylori dethiobiotin synthetase RT reveals differences between family members."; RL FEBS J. 279:1093-1105(2012). 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; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00336, ECO:0000269|PubMed:22284390}; CC Note=Binds 1 Mg(2+) per subunit, in some structures a second Mg(2+) is CC also seen. {ECO:0000269|PubMed:22284390}; 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|PubMed:22284390}. CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00336}. CC -!- DOMAIN: Substrate binds in a cavity formed at the dimer interface. CC {ECO:0000269|PubMed:22284390}. CC -!- SIMILARITY: Belongs to the dethiobiotin synthetase family. CC {ECO:0000255|HAMAP-Rule:MF_00336}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AE000511; AAD07100.1; -; Genomic_DNA. DR PIR; E64523; E64523. DR RefSeq; NP_206831.1; NC_000915.1. DR RefSeq; WP_000897490.1; NC_018939.1. DR PDB; 2QMO; X-ray; 1.47 A; A=1-218. DR PDB; 3MLE; X-ray; 2.80 A; A/B/C/D/E/F=1-218. DR PDB; 3QXC; X-ray; 1.34 A; A=1-218. DR PDB; 3QXH; X-ray; 1.36 A; A=1-218. DR PDB; 3QXJ; X-ray; 1.38 A; A=1-218. DR PDB; 3QXS; X-ray; 1.35 A; A=1-218. DR PDB; 3QXX; X-ray; 1.36 A; A=1-218. DR PDB; 3QY0; X-ray; 1.60 A; A=1-218. DR PDBsum; 2QMO; -. DR PDBsum; 3MLE; -. DR PDBsum; 3QXC; -. DR PDBsum; 3QXH; -. DR PDBsum; 3QXJ; -. DR PDBsum; 3QXS; -. DR PDBsum; 3QXX; -. DR PDBsum; 3QY0; -. DR AlphaFoldDB; O24872; -. DR SMR; O24872; -. DR MINT; O24872; -. DR STRING; 85962.HP_0029; -. DR PaxDb; 85962-C694_00135; -. DR EnsemblBacteria; AAD07100; AAD07100; HP_0029. DR KEGG; hpy:HP_0029; -. DR PATRIC; fig|85962.47.peg.30; -. DR eggNOG; COG0132; Bacteria. DR InParanoid; O24872; -. DR OrthoDB; 9802097at2; -. DR PhylomeDB; O24872; -. DR UniPathway; UPA00078; UER00161. DR EvolutionaryTrace; O24872; -. DR Proteomes; UP000000429; Chromosome. DR GO; GO:0005829; C:cytosol; IBA:GO_Central. 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; IBA:GO_Central. 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 SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 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..218 FT /note="ATP-dependent dethiobiotin synthetase BioD" FT /id="PRO_0000187971" FT ACT_SITE 35 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336, FT ECO:0000305|PubMed:22284390" FT BINDING 9..15 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336, FT ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, FT ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, FT ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS" FT BINDING 14 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336, FT ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, FT ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, FT ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS, FT ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0" FT BINDING 35 FT /ligand="phosphate" FT /ligand_id="ChEBI:CHEBI:43474" FT /evidence="ECO:0000269|PubMed:22284390, FT ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXH, FT ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0" FT BINDING 39 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336, FT ECO:0000269|PubMed:22284390" FT BINDING 50 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000269|PubMed:22284390, FT ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXC, FT ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXJ, FT ECO:0007744|PDB:3QXS" FT BINDING 50 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000269|PubMed:22284390, FT ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXC, FT ECO:0007744|PDB:3QXH, ECO:0007744|PDB:3QXJ, FT ECO:0007744|PDB:3QXS, ECO:0007744|PDB:3QXX, FT ECO:0007744|PDB:3QY0" FT BINDING 116..119 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336" FT BINDING 116..119 FT /ligand="phosphate" FT /ligand_id="ChEBI:CHEBI:43474" FT /evidence="ECO:0007744|PDB:3MLE, ECO:0007744|PDB:3QXH, FT ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0" FT BINDING 116 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000269|PubMed:22284390, FT ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXJ, FT ECO:0007744|PDB:3QXS" FT BINDING 116 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336, FT ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, FT ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXH, FT ECO:0007744|PDB:3QXJ, ECO:0007744|PDB:3QXS, FT ECO:0007744|PDB:3QXX, ECO:0007744|PDB:3QY0" FT BINDING 151..154 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:22284390, FT ECO:0007744|PDB:3MLE" FT BINDING 175..177 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336, FT ECO:0000269|PubMed:22284390, ECO:0007744|PDB:3MLE, FT ECO:0007744|PDB:3QXH" FT BINDING 175 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000269|PubMed:22284390, FT ECO:0007744|PDB:3QXC, ECO:0007744|PDB:3QXS" FT STRAND 1..8 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 13..26 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 31..34 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 37..40 FT /evidence="ECO:0007829|PDB:3MLE" FT TURN 43..45 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 50..59 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 67..70 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 76..79 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 81..88 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 96..105 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 106..108 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 111..116 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 118..120 FT /evidence="ECO:0007829|PDB:3QXH" FT STRAND 124..128 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 131..138 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 141..146 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 152..164 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 166..168 FT /evidence="ECO:0007829|PDB:3QXC" FT STRAND 170..174 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 182..186 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 188..197 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 205..207 FT /evidence="ECO:0007829|PDB:3QXC" FT HELIX 209..217 FT /evidence="ECO:0007829|PDB:3QXC" SQ SEQUENCE 218 AA; 24407 MW; C818F3D3A88C6015 CRC64; MLFISATNTN AGKTTCARLL AQYCNACGVK TILLKPIETG VNDAINHSSD AHLFLQDNRL LDRSLTLKDI SFYRYHKVSA PLIAQQEEDP NAPIDTDNLT QRLHNFTKTY DLVIVEGAGG LCVPITLEEN MLDFALKLKA KMLLISHDNL GLINDCLLND FLLKSHQLDY KIAINLKGNN TAFHSISLPY IELFNTRSNN PIVIFQQSLK VLMSFALK //