BIOD_HELPY
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 03-AUG-2022, entry version 126.
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=HP_0029;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; 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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00336,
CC 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}.
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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.C694_00135; -.
DR PaxDb; O24872; -.
DR EnsemblBacteria; AAD07100; AAD07100; HP_0029.
DR KEGG; hpy:HP_0029; -.
DR PATRIC; fig|85962.47.peg.30; -.
DR eggNOG; COG0132; Bacteria.
DR OMA; KMLLISH; -.
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 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 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..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
