P13000 (BIOD1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent dethiobiotin synthetase BioD 1
EC=6.3.3.3

Alternative name(s):
DTB synthetase 1
Short name=DTBS 1
Dethiobiotin synthase

Gene names

Name:	bioD1
Ordered Locus Names:	b0778, JW0761

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	225 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.6 Ref.7
Catalytic activity	ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin. Ref.7
Cofactor	Magnesium.
Pathway	Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2. HAMAP-Rule MF_00336
Subunit structure	Homodimer. Ref.7 Ref.9 Ref.10 Ref.13
Subcellular location	Cytoplasm HAMAP-Rule MF_00336.
Sequence similarities	Belongs to the dethiobiotin synthetase family.

Ontologies

Keywords
Biological process	Biotin biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	biotin biosynthetic process Inferred from mutant phenotype PubMed 4921685. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP dethiobiotin synthase activity Inferred from direct assay Ref.7. Source: UniProtKB magnesium ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.2

Chain

2 – 225

224

ATP-dependent dethiobiotin synthetase BioD 1 HAMAP-Rule MF_00336

PRO_0000187961

Regions

Nucleotide binding

13 – 18

6

ATP HAMAP-Rule MF_00336

Nucleotide binding

116 – 119

4

ATP HAMAP-Rule MF_00336

Nucleotide binding

176 – 177

2

ATP HAMAP-Rule MF_00336

Nucleotide binding

205 – 207

3

ATP HAMAP-Rule MF_00336

Sites

Metal binding

13

1

Magnesium 1

Metal binding

17

1

Magnesium 2

Metal binding

55

1

Magnesium 2

Metal binding

116

1

Magnesium 2

Binding site

42

1

Substrate

Binding site

55

1

ATP

Binding site

212

1

ATP

Experimental info

Mutagenesis

12

1

T → V: Strong decreased in the affinity for ATP; essential role for this residue in the steady-state affinity for ATP. Ref.8

Mutagenesis

13

1

E → A or D: Almost no change in activity. Ref.8

Mutagenesis

16

1

K → Q: Complete loss of activity. Ref.8

Mutagenesis

38

1

K → L, Q or R: Complete loss of activity. Ref.8

Mutagenesis

42

1

S → A or C: Almost no change in activity. Ref.8

Sequence conflict

29

1

A → R in AAA23518. Ref.1

Sequence conflict

108 – 109

2

QQ → HK in CAA00967. Ref.3

Sequence conflict

198 – 225

28

APLLG…NLALL → RRCWERSPGLQKIQKMRQPE ST in AAA23518. Ref.1

Secondary structure

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225

Helix Strand Turn

Details...

Beta strand

3 – 11

9

Helix

16 – 29

14

Beta strand

34 – 37

4

Beta strand

39 – 43

5

Beta strand

45 – 47

3

Beta strand

50 – 52

3

Helix

54 – 61

8

Beta strand

63 – 65

3

Helix

69 – 72

4

Beta strand

74 – 79

6

Helix

83 – 90

8

Helix

96 – 107

12

Beta strand

111 – 116

6

Beta strand

118 – 120

3

Beta strand

124 – 126

3

Helix

131 – 138

8

Beta strand

142 – 147

6

Helix

152 – 165

14

Beta strand

170 – 176

7

Helix

185 – 195

11

Beta strand

196 – 198

3

Beta strand

200 – 204

5

Turn

211 – 213

3

Helix

217 – 219

3

Helix

222 – 224

3

Sequences

	Sequence		Length	Mass (Da)
	P13000 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 9AE76F3BE6565780	FASTA	225	24,140
	10 20 30 40 50 60 MSKRYFVTGT DTEVGKTVAS CALLQAAKAA GYRTAGYKPV ASGSEKTPEG LRNSDALALQ 70 80 90 100 110 120 RNSSLQLDYA TVNPYTFAEP TSPHIISAQE GRPIESLVMS AGLRALEQQA DWVLVEGAGG 130 140 150 160 170 180 WFTPLSDTFT FADWVTQEQL PVILVVGVKL GCINHAMLTA QVIQHAGLTL AGWVANDVTP 190 200 210 220 PGKRHAEYMT TLTRMIPAPL LGEIPWLAEN PENAATGKYI NLALL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon." Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J. J. Biol. Chem. 263:19577-19585(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis." Alexeev D., Bury S.M., Boys C.W.G., Turner M.A., Sawyer L., Ramsey A.J., Baxter H.C., Baxter R.L. J. Mol. Biol. 235:774-776(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20 AND 224-225.
[3]	"Genetic material for expression of biotin synthetase enzymes." Pearson B.M., McKee R.A. Patent number GB2216530, 11-OCT-1989 Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12." Eisenberg M.A., Krell K. J. Bacteriol. 98:1227-1231(1969) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN BIOTIN BIOSYNTHESIS.
[7]	"The purification and properties of dethiobiotin synthetase." Krell K., Eisenberg M.A. J. Biol. Chem. 245:6558-6566(1970) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A DETHIOBIOTIN SYNTHETASE, CATALYTIC ACTIVITY, SUBSTRATES SPECIFICITY, SUBUNIT.
[8]	"Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties." Yang G., Sandalova T., Lohman K., Lindqvist Y., Rendina A.R. Biochemistry 36:4751-4760(1997) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF THR-12; GLU-13; LYS-16; LYS-38 AND SER-42.
[9]	"Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65-A resolution." Huang W., Lindqvist Y., Schneider G., Gibson K.J., Flint D., Lorimer G. Structure 2:407-414(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), SUBUNIT.
[10]	"Mechanistic implications and family relationships from the structure of dethiobiotin synthetase." Sawyer L., Baxter R.L., Alexeev D. Structure 2:1061-1072(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, SUBUNIT.
[11]	"Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate." Huang W., Jia J., Gibson K.J., Taylor W.S., Rendina A.R., Schneider G., Lindqvist Y. Biochemistry 34:10985-10995(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 2-224 IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, REACTION MECHANISM.
[12]	"Snapshot of a phosphorylated substrate intermediate by kinetic crystallography." Kaeck H., Gibson K.J., Lindqvist Y., Schneider G. Proc. Natl. Acad. Sci. U.S.A. 95:5495-5500(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP, MAGNESIUM IONS.
[13]	"Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis." Kaeck H., Sandmark J., Gibson K.J., Schneider G., Lindqvist Y. Protein Sci. 7:2560-2566(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, SUBUNIT.
[14]	"Structure of dethiobiotin synthetase at 0.97-A resolution." Sandalova T., Schneider G., Kack H., Lindqvist Y. Acta Crystallogr. D 55:610-624(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J04423 Genomic DNA. Translation: AAA23518.1.
S68059 Genomic DNA. Translation: AAB29683.2.
A11538 Unassigned DNA. Translation: CAA00967.1.
U00096 Genomic DNA. Translation: AAC73865.1.
AP009048 Genomic DNA. Translation: BAE76365.1.

PIR

SYECDB. B64814.

RefSeq

NP_415299.1. NC_000913.2.
YP_489051.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A82	X-ray	1.80	A	2-225	[»]
1BS1	X-ray	1.80	A	2-225	[»]
1BYI	X-ray	0.97	A	2-225	[»]
1DAD	X-ray	1.60	A	2-224	[»]
1DAE	X-ray	1.70	A	2-224	[»]
1DAF	X-ray	1.70	A	2-224	[»]
1DAG	X-ray	1.64	A	2-224	[»]
1DAH	X-ray	1.64	A	2-224	[»]
1DAI	X-ray	1.64	A	2-224	[»]
1DAK	X-ray	1.60	A	2-225	[»]
1DAM	X-ray	1.80	A	2-225	[»]
1DBS	X-ray	1.80	A	2-225	[»]
1DTS	X-ray	1.65	A	1-225	[»]

ProteinModelPortal

P13000.

SMR

P13000. Positions 2-225.

ModBase

Search...

Protein-protein interaction databases

IntAct

P13000. 3 interactions.

STRING

511145.b0778.

Proteomic databases

PaxDb

P13000.

PRIDE

P13000.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73865; AAC73865; b0778.
BAE76365; BAE76365; BAE76365.

GeneID

12930962.
945387.

KEGG

ecj:Y75_p0751.
eco:b0778.

PATRIC

32116757. VBIEscCol129921_0804.

Organism-specific databases

EchoBASE

EB0118.

EcoGene

EG10120. bioD1.

Phylogenomic databases

eggNOG

COG0132.

HOGENOM

HOG000275032.

KO

K01935.

OMA

AGWVANV.

ProtClustDB

PRK00090.

Enzyme and pathway databases

BioCyc

EcoCyc:DETHIOBIOTIN-SYN-MONOMER.
ECOL316407:JW0761-MONOMER.
MetaCyc:DETHIOBIOTIN-SYN-MONOMER.

SABIO-RK

P13000.

UniPathway

UPA00078; UER00161.

Gene expression databases

Genevestigator

P13000.

Family and domain databases

HAMAP

MF_00336. BioD.

InterPro

IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
IPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]

Pfam

PF01656. CbiA. 1 hit.
[Graphical view]

PIRSF

PIRSF006755. DTB_synth. 1 hit.

SUPFAM

SSF52540. SSF52540. 1 hit.

TIGRFAMs

TIGR00347. bioD. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P13000.

Entry information

Entry name

BIOD1_ECOLI

Accession

Primary (citable) accession number: P13000
Secondary accession number(s): Q2MBJ1

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 23, 2007
Last modified:	May 29, 2013
This is version 126 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program