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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: 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

Pathway:ibiotin 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi10 – 101Magnesium 1By similarity
Metal bindingi14 – 141Magnesium 2
Binding sitei35 – 351ATP
Binding sitei39 – 391Substrate
Metal bindingi50 – 501Magnesium 2
Binding sitei50 – 501ATP
Binding sitei63 – 631ATP
Metal bindingi116 – 1161Magnesium 2
Binding sitei175 – 1751ATP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 157ATP
Nucleotide bindingi116 – 1194ATP
Nucleotide bindingi151 – 1544Substrate

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
ProteomesiUP000000429 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 218218ATP-dependent dethiobiotin synthetase BioDPRO_0000187971Add
BLAST

Proteomic databases

PRIDEiO24872.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

MINTiMINT-8303355.
STRINGi85962.HP0029.

Structurei

Secondary structure

218
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 88Combined sources
Helixi13 – 2614Combined sources
Beta strandi31 – 344Combined sources
Beta strandi37 – 404Combined sources
Turni43 – 453Combined sources
Helixi50 – 5910Combined sources
Helixi67 – 704Combined sources
Beta strandi76 – 794Combined sources
Helixi81 – 888Combined sources
Helixi96 – 10510Combined sources
Helixi106 – 1083Combined sources
Beta strandi111 – 1166Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi124 – 1285Combined sources
Helixi131 – 1388Combined sources
Beta strandi141 – 1466Combined sources
Helixi152 – 16413Combined sources
Beta strandi166 – 1683Combined sources
Beta strandi170 – 1745Combined sources
Helixi182 – 1865Combined sources
Helixi188 – 19710Combined sources
Helixi205 – 2073Combined sources
Helixi209 – 2179Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-218.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO24872.

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.Curated

Phylogenomic databases

eggNOGiCOG0132.
KOiK01935.
OMAiGLCVPIT.
OrthoDBiEOG66B3XT.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD.
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
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. Positions 1-218.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-8303355.
STRINGi85962.HP0029.

Proteomic databases

PRIDEiO24872.

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

eggNOGiCOG0132.
KOiK01935.
OMAiGLCVPIT.
OrthoDBiEOG66B3XT.

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

Publicationsi

« Hide 'large scale' publications
  1. 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 SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, SUBUNIT.

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: July 22, 2015
This is version 97 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

External Data

Dasty 3

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 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.