Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-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

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Biotin biosynthesis

Keywords - Ligandi

ATP-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

Complete GO annotation...

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

MINTiMINT-8303355.
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.
OMAiNPIVIFQ.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD. 1 hit.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
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.
PATRICi20591257. VBIHelPyl33062_0030.

Cross-referencesi

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.

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...

Protein-protein interaction databases

MINTiMINT-8303355.
STRINGi85962.HP0029.

Proteomic databases

PaxDbiO24872.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07100; AAD07100; HP_0029.
GeneIDi899125.
KEGGiheo:C694_00135.
hpy:HP0029.
PATRICi20591257. VBIHelPyl33062_0030.

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
KOiK01935.
OMAiNPIVIFQ.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciHPY:HP0029-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO24872.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD. 1 hit.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00347. bioD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiBIOD_HELPY
AccessioniPrimary (citable) accession number: O24872
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.