Q5DZI1 (BIOD_VIBF1) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

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

Gene names

Name:	bioD
Ordered Locus Names:	VF_A0745

Organism

Vibrio fischeri (strain ATCC 700601 / ES114)

Taxonomic identifier

312309 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Aliivibrio

Protein attributes

Sequence length	226 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 By similarity. HAMAP MF_00336
Catalytic activity	ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin. HAMAP MF_00336
Cofactor	Magnesium By similarity. HAMAP MF_00336
Pathway	Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2. HAMAP MF_00336
Subcellular location	Cytoplasm By similarity HAMAP 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	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	biotin biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW dethiobiotin synthase activity Inferred from electronic annotation. Source: EC magnesium ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 226	226	ATP-dependent dethiobiotin synthetase BioD HAMAP MF_00336		PRO_0000302552
Regions
	Nucleotide binding	13 – 18	6	ATP By similarity
	Nucleotide binding	116 – 119	4	ATP By similarity
	Nucleotide binding	176 – 177	2	ATP By similarity
Sites
	Metal binding	13	1	Magnesium 1 By similarity
	Metal binding	17	1	Magnesium 2 By similarity
	Metal binding	55	1	Magnesium 2 By similarity
	Metal binding	116	1	Magnesium 2 By similarity
	Binding site	55	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5DZI1 [UniParc]. Last modified March 15, 2005. Version 1. Checksum: 43B797D856C363C1	FASTA	226	24,409
	10 20 30 40 50 60 MIDAFFIAGT DTDVGKTVAS KAILDALNMK GLRTAAYKPV AAGSEDKGEG VQNSDAIHLR 70 80 90 100 110 120 AVANVELRYE EVNPYALLMP ASPHIAAEAE NVVIDYSVLS EGLASLKEKS DVVLVEGAGG 130 140 150 160 170 180 WRVPVSKDDC LSTWVQQEKL PVVLVVGIKL GCLSHAMLTA EAIQHDGLEI IGWVANRVNP 190 200 210 220 GTENYAEIIK MLEDKMPAPK LGEIPYMPSV KRKNMGKYIH LEALDN

References

[1]

"Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners." Ruby E.G., Urbanowski M., Campbell J., Dunn A., Faini M., Gunsalus R., Lostroh P., Lupp C., McCann J., Millikan D., Schaefer A., Stabb E., Stevens A., Visick K., Whistler C., Greenberg E.P. Proc. Natl. Acad. Sci. U.S.A. 102:3004-3009(2005) [PubMed: 15703294] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700601 / ES114.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000021 Genomic DNA. Translation: AAW87815.1.
RefSeq	YP_206703.1. NC_006841.2.
3D structure databases
HSSP	HSSP built from PDB template 1DTS based on UniProtKB P13000.
ProteinModelPortal	Q5DZI1.
ModBase	Search...
Protein-protein interaction databases
STRING	Q5DZI1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3280456.
GenomeReviews	Gene locus VF_A0745 in contig CP000021_GR.
KEGG	vfi:VF_A0745.
NMPDR	fig|312309.3.peg.3601.
PATRIC	20117485. VBIVibFis127983_3346.
Phylogenomic databases
eggNOG	COG0132.
HOGENOM	HBG650065.
OMA	AEAVGWC.
PhylomeDB	Q5DZI1.
ProtClustDB	PRK00090.
Enzyme and pathway databases
BioCyc	VFIS312309:VFA0745-MONOMER.
Family and domain databases
HAMAP	MF_00336. BioD. [Tree]
InterPro	IPR002586. CbiA_P_synth. IPR004472. DTB_synth_BioD. [Graphical view]
KO	K01935.
Pfam	PF01656. CbiA. 1 hit. [Graphical view]
PIRSF	PIRSF006755. DTB_synth. 1 hit.
TIGRFAMs	TIGR00347. BioD. 1 hit.
ProtoNet	Search...

Entry information

Entry name

BIOD_VIBF1

Accession

Primary (citable) accession number: Q5DZI1

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	March 15, 2005
Last modified:	January 25, 2012
This is version 44 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program