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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-JUL-2017, entry version 154.
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: ATP + 7,8-diaminononanoate + CO(2) = ADP +
phosphate + dethiobiotin. {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; 11.
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.
NP_BIND 116 119 ATP.
NP_BIND 176 177 ATP.
NP_BIND 205 207 ATP.
METAL 13 13 Magnesium 1.
METAL 17 17 Magnesium 2.
METAL 55 55 Magnesium 2.
METAL 116 116 Magnesium 2.
BINDING 42 42 Substrate.
BINDING 55 55 ATP.
BINDING 212 212 ATP.
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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