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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin.

Cofactori

Mg2+By similarity

Pathwayi: biotin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes biotin from 7,8-diaminononanoate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. ATP-dependent dethiobiotin synthetase BioD (bioD)
  2. Biotin synthase (bioB)
This subpathway is part of the pathway biotin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes biotin from 7,8-diaminononanoate, the pathway biotin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi10Magnesium 1By similarity1
Metal bindingi14Magnesium 21
Binding sitei35ATP1
Binding sitei39Substrate1
Metal bindingi50Magnesium 21
Binding sitei50ATP1
Binding sitei63ATP1
Metal bindingi116Magnesium 21
Binding sitei175ATP1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi9 – 15ATP7
Nucleotide bindingi116 – 119ATP4
Nucleotide bindingi151 – 154Substrate4

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processBiotin biosynthesis
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciHPY:HP0029-MONOMER
UniPathwayiUPA00078; UER00161

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent dethiobiotin synthetase BioD (EC:6.3.3.3)
Alternative name(s):
DTB synthetase
Short name:
DTBS
Dethiobiotin synthase
Gene namesi
Name:bioD
Ordered Locus Names:HP_0029
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000429 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001879711 – 218ATP-dependent dethiobiotin synthetase BioDAdd BLAST218

Proteomic databases

PaxDbiO24872

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

MINTiO24872
STRINGi85962.HP0029

Structurei

Secondary structure

1218
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 8Combined sources8
Helixi13 – 26Combined sources14
Beta strandi31 – 34Combined sources4
Beta strandi37 – 40Combined sources4
Turni43 – 45Combined sources3
Helixi50 – 59Combined sources10
Helixi67 – 70Combined sources4
Beta strandi76 – 79Combined sources4
Helixi81 – 88Combined sources8
Helixi96 – 105Combined sources10
Helixi106 – 108Combined sources3
Beta strandi111 – 116Combined sources6
Beta strandi118 – 120Combined sources3
Beta strandi124 – 128Combined sources5
Helixi131 – 138Combined sources8
Beta strandi141 – 146Combined sources6
Helixi152 – 164Combined sources13
Beta strandi166 – 168Combined sources3
Beta strandi170 – 174Combined sources5
Helixi182 – 186Combined sources5
Helixi188 – 197Combined sources10
Helixi205 – 207Combined sources3
Helixi209 – 217Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2QMOX-ray1.47A1-218[»]
3MLEX-ray2.80A/B/C/D/E/F1-218[»]
3QXCX-ray1.34A1-218[»]
3QXHX-ray1.36A1-218[»]
3QXJX-ray1.38A1-218[»]
3QXSX-ray1.35A1-218[»]
3QXXX-ray1.36A1-218[»]
3QY0X-ray1.60A1-218[»]
ProteinModelPortaliO24872
SMRiO24872
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO24872

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.Curated

Phylogenomic databases

eggNOGiENOG4105E78 Bacteria
COG0132 LUCA
KOiK01935
OMAiKMLLISH

Family and domain databases

HAMAPiMF_00336 BioD, 1 hit
InterProiView protein in InterPro
IPR004472 DTB_synth_BioD
IPR027417 P-loop_NTPase
PANTHERiPTHR43210 PTHR43210, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR00347 bioD, 1 hit

Sequencei

Sequence statusi: Complete.

O24872-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLFISATNTN AGKTTCARLL AQYCNACGVK TILLKPIETG VNDAINHSSD
60 70 80 90 100
AHLFLQDNRL LDRSLTLKDI SFYRYHKVSA PLIAQQEEDP NAPIDTDNLT
110 120 130 140 150
QRLHNFTKTY DLVIVEGAGG LCVPITLEEN MLDFALKLKA KMLLISHDNL
160 170 180 190 200
GLINDCLLND FLLKSHQLDY KIAINLKGNN TAFHSISLPY IELFNTRSNN
210
PIVIFQQSLK VLMSFALK
Length:218
Mass (Da):24,407
Last modified:January 1, 1998 - v1
Checksum:iC818F3D3A88C6015
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA Translation: AAD07100.1
PIRiE64523
RefSeqiNP_206831.1, NC_000915.1
WP_000897490.1, NC_018939.1

Genome annotation databases

EnsemblBacteriaiAAD07100; AAD07100; HP_0029
GeneIDi899125
KEGGiheo:C694_00135
hpy:HP0029
PATRICifig|85962.47.peg.30

Similar proteinsi

Entry informationi

Entry nameiBIOD_HELPY
AccessioniPrimary (citable) accession number: O24872
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: March 28, 2018
This is version 109 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health