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ATP-dependent dethiobiotin synthetase BioD 1 (EC 6.3.3.3) (DTB synthetase 1) (DTBS 1) (Dethiobiotin synthase)

 BIOD1_ECOLI             Reviewed;         225 AA.
P13000; Q2MBJ1;
01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
05-DEC-2018, entry version 158.
RecName: Full=ATP-dependent dethiobiotin synthetase BioD 1;
EC=6.3.3.3;
AltName: Full=DTB synthetase 1;
Short=DTBS 1;
AltName: Full=Dethiobiotin synthase;
Name=bioD1; OrderedLocusNames=b0778, JW0761;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3058702;
Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O.,
Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.;
"The Escherichia coli biotin biosynthetic enzyme sequences predicted
from the nucleotide sequence of the bio operon.";
J. Biol. Chem. 263:19577-19585(1988).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-20 AND
224-225.
PubMed=8289297; DOI=10.1006/jmbi.1994.1030;
Alexeev D., Bury S.M., Boys C.W.G., Turner M.A., Sawyer L.,
Ramsey A.J., Baxter H.C., Baxter R.L.;
"Sequence and crystallization of Escherichia coli dethiobiotin
synthetase, the penultimate enzyme of biotin biosynthesis.";
J. Mol. Biol. 235:774-776(1994).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Pearson B.M., McKee R.A.;
"Genetic material for expression of biotin synthetase enzymes.";
Patent number GB2216530, 11-OCT-1989.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
FUNCTION IN BIOTIN BIOSYNTHESIS.
PubMed=4892372;
Eisenberg M.A., Krell K.;
"Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin
auxotrophs of Escherichia coli K-12.";
J. Bacteriol. 98:1227-1231(1969).
[7]
FUNCTION AS A DETHIOBIOTIN SYNTHETASE, CATALYTIC ACTIVITY, SUBSTRATE
SPECIFICITY, AND SUBUNIT.
PubMed=4921568;
Krell K., Eisenberg M.A.;
"The purification and properties of dethiobiotin synthetase.";
J. Biol. Chem. 245:6558-6566(1970).
[8]
MUTAGENESIS OF THR-12; GLU-13; LYS-16; LYS-38 AND SER-42.
PubMed=9125495; DOI=10.1021/bi9631677;
Yang G., Sandalova T., Lohman K., Lindqvist Y., Rendina A.R.;
"Active site mutants of Escherichia coli dethiobiotin synthetase:
effects of mutations on enzyme catalytic and structural properties.";
Biochemistry 36:4751-4760(1997).
[9]
X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), AND SUBUNIT.
PubMed=8081756; DOI=10.1016/S0969-2126(00)00042-3;
Huang W., Lindqvist Y., Schneider G., Gibson K.J., Flint D.,
Lorimer G.;
"Crystal structure of an ATP-dependent carboxylase, dethiobiotin
synthetase, at 1.65-A resolution.";
Structure 2:407-414(1994).
[10]
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE
ANALOGS, ATP AND MAGNESIUM IONS, AND SUBUNIT.
PubMed=7881906; DOI=10.1016/S0969-2126(94)00109-X;
Sawyer L., Baxter R.L., Alexeev D.;
"Mechanistic implications and family relationships from the structure
of dethiobiotin synthetase.";
Structure 2:1061-1072(1994).
[11]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 2-224 IN COMPLEX WITH
SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, AND REACTION MECHANISM.
PubMed=7669756; DOI=10.1021/bi00035a004;
Huang W., Jia J., Gibson K.J., Taylor W.S., Rendina A.R.,
Schneider G., Lindqvist Y.;
"Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase,
based on crystallographic studies of complexes with substrates and a
reaction intermediate.";
Biochemistry 34:10985-10995(1995).
[12]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH SUBSTRATE
ANALOGS, ATP, AND MAGNESIUM IONS.
PubMed=9576910; DOI=10.1073/pnas.95.10.5495;
Kaeck H., Gibson K.J., Lindqvist Y., Schneider G.;
"Snapshot of a phosphorylated substrate intermediate by kinetic
crystallography.";
Proc. Natl. Acad. Sci. U.S.A. 95:5495-5500(1998).
[13]
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE
ANALOGS, ATP AND MAGNESIUM IONS, AND SUBUNIT.
PubMed=9865950; DOI=10.1002/pro.5560071209;
Kaeck H., Sandmark J., Gibson K.J., Schneider G., Lindqvist Y.;
"Crystal structure of two quaternary complexes of dethiobiotin
synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-
dethiobiotin-phosphate; implications for catalysis.";
Protein Sci. 7:2560-2566(1998).
[14]
X-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS).
PubMed=10089457; DOI=10.1107/S090744499801381X;
Sandalova T., Schneider G., Kack H., Lindqvist Y.;
"Structure of dethiobiotin synthetase at 0.97-A resolution.";
Acta Crystallogr. D 55:610-624(1999).
-!- FUNCTION: Catalyzes a mechanistically unusual reaction, the ATP-
dependent insertion of CO2 between the N7 and N8 nitrogen atoms of
7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP
can partially replace ATP while diaminobiotin is only 37% as
effective as 7,8-diaminopelargonic acid.
{ECO:0000269|PubMed:4892372, ECO:0000269|PubMed:4921568}.
-!- CATALYTIC ACTIVITY:
Reaction=7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 3
H(+) + phosphate; Xref=Rhea:RHEA:15805, ChEBI:CHEBI:15378,
ChEBI:CHEBI:16526, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
ChEBI:CHEBI:57861, ChEBI:CHEBI:58500, ChEBI:CHEBI:456216;
EC=6.3.3.3; Evidence={ECO:0000269|PubMed:4921568};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
-!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from
7,8-diaminononanoate: step 1/2.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:4921568,
ECO:0000269|PubMed:7669756, ECO:0000269|PubMed:7881906,
ECO:0000269|PubMed:8081756, ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- SIMILARITY: Belongs to the dethiobiotin synthetase family.
{ECO:0000305}.
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EMBL; J04423; AAA23518.1; -; Genomic_DNA.
EMBL; S68059; AAB29683.2; -; Genomic_DNA.
EMBL; A11538; CAA00967.1; -; Unassigned_DNA.
EMBL; U00096; AAC73865.1; -; Genomic_DNA.
EMBL; AP009048; BAE76365.1; -; Genomic_DNA.
PIR; B64814; SYECDB.
RefSeq; NP_415299.1; NC_000913.3.
RefSeq; WP_000044843.1; NZ_LN832404.1.
PDB; 1A82; X-ray; 1.80 A; A=2-225.
PDB; 1BS1; X-ray; 1.80 A; A=2-225.
PDB; 1BYI; X-ray; 0.97 A; A=2-225.
PDB; 1DAD; X-ray; 1.60 A; A=2-225.
PDB; 1DAE; X-ray; 1.70 A; A=2-225.
PDB; 1DAF; X-ray; 1.70 A; A=2-225.
PDB; 1DAG; X-ray; 1.64 A; A=2-225.
PDB; 1DAH; X-ray; 1.64 A; A=2-225.
PDB; 1DAI; X-ray; 1.64 A; A=2-225.
PDB; 1DAK; X-ray; 1.60 A; A=2-225.
PDB; 1DAM; X-ray; 1.80 A; A=2-225.
PDB; 1DBS; X-ray; 1.80 A; A=2-225.
PDB; 1DTS; X-ray; 1.65 A; A=1-224.
PDBsum; 1A82; -.
PDBsum; 1BS1; -.
PDBsum; 1BYI; -.
PDBsum; 1DAD; -.
PDBsum; 1DAE; -.
PDBsum; 1DAF; -.
PDBsum; 1DAG; -.
PDBsum; 1DAH; -.
PDBsum; 1DAI; -.
PDBsum; 1DAK; -.
PDBsum; 1DAM; -.
PDBsum; 1DBS; -.
PDBsum; 1DTS; -.
ProteinModelPortal; P13000; -.
SMR; P13000; -.
BioGrid; 4259956; 20.
IntAct; P13000; 3.
STRING; 316385.ECDH10B_0846; -.
DrugBank; DB02941; 3-(1-Aminoethyl)Nonanedioic Acid.
DrugBank; DB03624; 7-(Carboxyamino)-8-Amino-Nonanoic Acid.
DrugBank; DB03775; D-Dethiobiotin.
PaxDb; P13000; -.
PRIDE; P13000; -.
EnsemblBacteria; AAC73865; AAC73865; b0778.
EnsemblBacteria; BAE76365; BAE76365; BAE76365.
GeneID; 945387; -.
KEGG; ecj:JW0761; -.
KEGG; eco:b0778; -.
PATRIC; fig|1411691.4.peg.1500; -.
EchoBASE; EB0118; -.
EcoGene; EG10120; bioD1.
eggNOG; ENOG4105E78; Bacteria.
eggNOG; COG0132; LUCA.
HOGENOM; HOG000275032; -.
InParanoid; P13000; -.
KO; K01935; -.
PhylomeDB; P13000; -.
BioCyc; EcoCyc:DETHIOBIOTIN-SYN-MONOMER; -.
BioCyc; MetaCyc:DETHIOBIOTIN-SYN-MONOMER; -.
SABIO-RK; P13000; -.
UniPathway; UPA00078; UER00161.
EvolutionaryTrace; P13000; -.
PRO; PR:P13000; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0005524; F:ATP binding; IDA:UniProtKB.
GO; GO:0004141; F:dethiobiotin synthase activity; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0009102; P:biotin biosynthetic process; IDA:UniProtKB.
HAMAP; MF_00336; BioD; 1.
InterPro; IPR004472; DTB_synth_BioD.
InterPro; IPR027417; P-loop_NTPase.
PANTHER; PTHR43210; PTHR43210; 1.
PIRSF; PIRSF006755; DTB_synth; 1.
SUPFAM; SSF52540; SSF52540; 1.
TIGRFAMs; TIGR00347; bioD; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Biotin biosynthesis; Complete proteome;
Cytoplasm; Direct protein sequencing; Ligase; Magnesium;
Metal-binding; Nucleotide-binding; Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:8289297}.
CHAIN 2 225 ATP-dependent dethiobiotin synthetase
BioD 1.
/FTId=PRO_0000187961.
NP_BIND 13 18 ATP. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAD,
ECO:0000244|PDB:1DAF,
ECO:0000244|PDB:1DAG,
ECO:0000244|PDB:1DAH,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:7669756,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
NP_BIND 116 119 ATP. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1DAK,
ECO:0000269|PubMed:9576910}.
NP_BIND 176 177 ATP. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAD,
ECO:0000244|PDB:1DAF,
ECO:0000244|PDB:1DAG,
ECO:0000244|PDB:1DAH,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:7669756,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
NP_BIND 205 207 ATP. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAD,
ECO:0000244|PDB:1DAF,
ECO:0000244|PDB:1DAG,
ECO:0000244|PDB:1DAH,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:7669756,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
METAL 13 13 Magnesium 1. {ECO:0000244|PDB:1BS1,
ECO:0000269|PubMed:9865950}.
METAL 17 17 Magnesium 2. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
METAL 55 55 Magnesium 2. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
METAL 116 116 Magnesium 2. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
BINDING 42 42 Substrate. {ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAE,
ECO:0000244|PDB:1DAF,
ECO:0000244|PDB:1DAG,
ECO:0000244|PDB:1DAH,
ECO:0000244|PDB:1DAI,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:7669756,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
BINDING 55 55 ATP. {ECO:0000244|PDB:1A82,
ECO:0000269|PubMed:9576910}.
BINDING 188 188 Substrate. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAE,
ECO:0000244|PDB:1DAF,
ECO:0000244|PDB:1DAG,
ECO:0000244|PDB:1DAH,
ECO:0000244|PDB:1DAI,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:7669756,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
BINDING 212 212 ATP. {ECO:0000244|PDB:1A82,
ECO:0000244|PDB:1BS1,
ECO:0000244|PDB:1DAD,
ECO:0000244|PDB:1DAF,
ECO:0000244|PDB:1DAH,
ECO:0000244|PDB:1DAK,
ECO:0000244|PDB:1DAM,
ECO:0000269|PubMed:7669756,
ECO:0000269|PubMed:9576910,
ECO:0000269|PubMed:9865950}.
MUTAGEN 12 12 T->V: Strong decreased in the affinity
for ATP; essential role for this residue
in the steady-state affinity for ATP.
{ECO:0000269|PubMed:9125495}.
MUTAGEN 13 13 E->A,D: Almost no change in activity.
{ECO:0000269|PubMed:9125495}.
MUTAGEN 16 16 K->Q: Complete loss of activity.
{ECO:0000269|PubMed:9125495}.
MUTAGEN 38 38 K->L,Q,R: Complete loss of activity.
{ECO:0000269|PubMed:9125495}.
MUTAGEN 42 42 S->A,C: Almost no change in activity.
{ECO:0000269|PubMed:9125495}.
CONFLICT 29 29 A -> R (in Ref. 1; AAA23518).
{ECO:0000305}.
CONFLICT 108 109 QQ -> HK (in Ref. 3; CAA00967).
{ECO:0000305}.
CONFLICT 198 225 APLLGEIPWLAENPENAATGKYINLALL -> RRCWERSPG
LQKIQKMRQPEST (in Ref. 1; AAA23518).
{ECO:0000305}.
STRAND 3 11 {ECO:0000244|PDB:1BYI}.
HELIX 16 29 {ECO:0000244|PDB:1BYI}.
STRAND 34 37 {ECO:0000244|PDB:1BYI}.
STRAND 39 43 {ECO:0000244|PDB:1BYI}.
STRAND 45 47 {ECO:0000244|PDB:1DAI}.
STRAND 50 52 {ECO:0000244|PDB:1DAI}.
HELIX 54 61 {ECO:0000244|PDB:1BYI}.
STRAND 63 65 {ECO:0000244|PDB:1DAD}.
HELIX 69 72 {ECO:0000244|PDB:1BYI}.
STRAND 74 79 {ECO:0000244|PDB:1BYI}.
HELIX 83 90 {ECO:0000244|PDB:1BYI}.
HELIX 96 107 {ECO:0000244|PDB:1BYI}.
STRAND 111 116 {ECO:0000244|PDB:1BYI}.
STRAND 118 120 {ECO:0000244|PDB:1BYI}.
STRAND 124 126 {ECO:0000244|PDB:1BYI}.
HELIX 131 138 {ECO:0000244|PDB:1BYI}.
STRAND 142 147 {ECO:0000244|PDB:1BYI}.
HELIX 152 165 {ECO:0000244|PDB:1BYI}.
STRAND 170 176 {ECO:0000244|PDB:1BYI}.
HELIX 185 195 {ECO:0000244|PDB:1BYI}.
STRAND 196 198 {ECO:0000244|PDB:1BYI}.
STRAND 200 204 {ECO:0000244|PDB:1BYI}.
TURN 211 213 {ECO:0000244|PDB:1DAD}.
HELIX 217 219 {ECO:0000244|PDB:1BYI}.
HELIX 222 224 {ECO:0000244|PDB:1BYI}.
SEQUENCE 225 AA; 24140 MW; 9AE76F3BE6565780 CRC64;
MSKRYFVTGT DTEVGKTVAS CALLQAAKAA GYRTAGYKPV ASGSEKTPEG LRNSDALALQ
RNSSLQLDYA TVNPYTFAEP TSPHIISAQE GRPIESLVMS AGLRALEQQA DWVLVEGAGG
WFTPLSDTFT FADWVTQEQL PVILVVGVKL GCINHAMLTA QVIQHAGLTL AGWVANDVTP
PGKRHAEYMT TLTRMIPAPL LGEIPWLAEN PENAATGKYI NLALL


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10-288-22051F Prostaglandin-H2 D-isomerase - EC 5.3.99.2; Lipocalin-type prostaglandin-D synthase; Glutathione-independent PGD synthetase; Prostaglandin-D2 synthase; PGD2 synthase; PGDS2; PGDS; Beta-trace protein; 0.1 mg
10-288-22051F Prostaglandin-H2 D-isomerase - EC 5.3.99.2; Lipocalin-type prostaglandin-D synthase; Glutathione-independent PGD synthetase; Prostaglandin-D2 synthase; PGD2 synthase; PGDS2; PGDS; Beta-trace protein; 0.05 mg
EIAAB31988 Coab,Mouse,Mus musculus,Phosphopantothenate--cysteine ligase,Phosphopantothenoylcysteine synthetase,PPC synthetase,Ppcs


 

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