O24872 (BIOD_HELPY) 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:	HP_0029

Organism

Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]

Taxonomic identifier

85962 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Helicobacter › Helicobacter pylori

Protein attributes

Sequence length	218 AA.
Sequence status	Complete.
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 By similarity. HAMAP-Rule MF_00336
Catalytic activity	ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin. HAMAP-Rule MF_00336
Cofactor	Magnesium By similarity.
Pathway	Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2. HAMAP-Rule MF_00336
Subunit structure	Homodimer. Ref.3
Subcellular location	Cytoplasm By similarity.
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 Reference proteome
Gene Ontology (GO)
Biological_process	biotin biosynthetic process Inferred from electronic annotation. Source: HAMAP
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 sequence or structural similarity. 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

Chain

1 – 218

218

ATP-dependent dethiobiotin synthetase BioD HAMAP-Rule MF_00336

PRO_0000187971

Regions

Nucleotide binding

9 – 15

7

ATP HAMAP-Rule MF_00336

Nucleotide binding

116 – 119

4

ATP HAMAP-Rule MF_00336

Nucleotide binding

151 – 154

4

Substrate HAMAP-Rule MF_00336

Sites

Metal binding

10

1

Magnesium 1 By similarity

Metal binding

14

1

Magnesium 2

Metal binding

50

1

Magnesium 2

Metal binding

116

1

Magnesium 2

Binding site

35

1

ATP

Binding site

39

1

Substrate

Binding site

50

1

ATP

Binding site

63

1

ATP

Binding site

175

1

ATP

Secondary structure

1

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218

Helix Strand Turn

Details...

Beta strand

1 – 8

8

Helix

13 – 26

14

Beta strand

31 – 34

4

Beta strand

37 – 40

4

Turn

43 – 45

3

Helix

50 – 59

10

Helix

67 – 70

4

Beta strand

76 – 79

4

Helix

81 – 88

8

Helix

96 – 105

10

Helix

106 – 108

3

Beta strand

111 – 116

6

Beta strand

118 – 120

3

Beta strand

124 – 128

5

Helix

131 – 138

8

Beta strand

141 – 146

6

Helix

152 – 164

13

Beta strand

166 – 168

3

Beta strand

170 – 174

5

Helix

182 – 186

5

Helix

188 – 197

10

Helix

205 – 207

3

Helix

209 – 217

9

Sequences

	Sequence		Length	Mass (Da)
	O24872 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: C818F3D3A88C6015	FASTA	218	24,407
	10 20 30 40 50 60 MLFISATNTN AGKTTCARLL AQYCNACGVK TILLKPIETG VNDAINHSSD AHLFLQDNRL 70 80 90 100 110 120 LDRSLTLKDI SFYRYHKVSA PLIAQQEEDP NAPIDTDNLT QRLHNFTKTY DLVIVEGAGG 130 140 150 160 170 180 LCVPITLEEN MLDFALKLKA KMLLISHDNL GLINDCLLND FLLKSHQLDY KIAINLKGNN 190 200 210 TAFHSISLPY IELFNTRSNN PIVIFQQSLK VLMSFALK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of the gastric pathogen Helicobacter pylori." Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C. Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700392 / 26695.
[2]	"Crystal structure of dethiobiotin synthetase (biod) from Helicobacter pylori." Midwest center for structural genomics (MCSG) Submitted (MAR-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS).
[3]	"Crystal structure of dethiobiotin synthetase (biod) from Helicobacter pylori cocrystallized with ATP." Midwest center for structural genomics (MCSG) Submitted (MAY-2010) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000511 Genomic DNA. Translation: AAD07100.1.

PIR

E64523.

RefSeq

NP_206831.1. NC_000915.1.
YP_006933951.1. NC_018939.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2QMO	X-ray	1.47	A	1-218	[»]
3MLE	X-ray	2.80	A/B/C/D/E/F	1-218	[»]
3QXC	X-ray	1.34	A	1-218	[»]
3QXH	X-ray	1.36	A	1-218	[»]
3QXJ	X-ray	1.38	A	1-218	[»]
3QXS	X-ray	1.35	A	1-218	[»]
3QXX	X-ray	1.36	A	1-218	[»]
3QY0	X-ray	1.60	A	1-218	[»]

ProteinModelPortal

O24872.

SMR

O24872. Positions 1-218.

ModBase

Search...

Protein-protein interaction databases

STRING

85962.HP0029.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD07100; AAD07100; HP_0029.

GeneID

13869205.
899125.

KEGG

heo:C694_00135.
hpy:HP0029.

PATRIC

20591257. VBIHelPyl33062_0030.

Phylogenomic databases

eggNOG

COG0132.

KO

K01935.

OMA

GLCVPIT.

ProtClustDB

CLSK495825.

Enzyme and pathway databases

UniPathway

UPA00078; UER00161.

Family and domain databases

HAMAP

MF_00336. BioD.

InterPro

IPR004472. DTB_synth_BioD.
[Graphical view]

PIRSF

PIRSF006755. DTB_synth. 1 hit.

TIGRFAMs

TIGR00347. bioD. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

O24872.

Entry information

Entry name

BIOD_HELPY

Accession

Primary (citable) accession number: O24872

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	January 1, 1998
Last modified:	May 1, 2013
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program