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O24872

- BIOD_HELPY

UniProt

O24872 - BIOD_HELPY

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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene
bioD, HP_0029
Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed - Annotation score: 5 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.UniRule annotation

Catalytic activityi

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

Cofactori

Magnesium By similarity.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi10 – 101Magnesium 1 By 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 – 157ATPUniRule annotation
Nucleotide bindingi116 – 1194ATPUniRule annotation
Nucleotide bindingi151 – 1544SubstrateUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. dethiobiotin synthase activity Source: UniProtKB
  3. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. biotin biosynthetic process Source: UniProtKB-HAMAP
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: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 218218ATP-dependent dethiobiotin synthetase BioDUniRule annotationPRO_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 – 88
Helixi13 – 2614
Beta strandi31 – 344
Beta strandi37 – 404
Turni43 – 453
Helixi50 – 5910
Helixi67 – 704
Beta strandi76 – 794
Helixi81 – 888
Helixi96 – 10510
Helixi106 – 1083
Beta strandi111 – 1166
Beta strandi118 – 1203
Beta strandi124 – 1285
Helixi131 – 1388
Beta strandi141 – 1466
Helixi152 – 16413
Beta strandi166 – 1683
Beta strandi170 – 1745
Helixi182 – 1865
Helixi188 – 19710
Helixi205 – 2073
Helixi209 – 2179

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiO24872.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0132.
KOiK01935.
OMAiEENMLDF.
OrthoDBiEOG66B3XT.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
PIRSFiPIRSF006755. DTB_synth. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00347. bioD. 1 hit.

Sequencei

Sequence statusi: Complete.

O24872-1 [UniParc]FASTAAdd to Basket

« Hide

MLFISATNTN AGKTTCARLL AQYCNACGVK TILLKPIETG VNDAINHSSD    50
AHLFLQDNRL LDRSLTLKDI SFYRYHKVSA PLIAQQEEDP NAPIDTDNLT 100
QRLHNFTKTY DLVIVEGAGG LCVPITLEEN MLDFALKLKA KMLLISHDNL 150
GLINDCLLND FLLKSHQLDY KIAINLKGNN TAFHSISLPY IELFNTRSNN 200
PIVIFQQSLK VLMSFALK 218
Length:218
Mass (Da):24,407
Last modified:January 1, 1998 - v1
Checksum:iC818F3D3A88C6015
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE000511 Genomic DNA. Translation: AAD07100.1.
PIRiE64523.
RefSeqiNP_206831.1. NC_000915.1.
YP_006933951.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD07100; AAD07100; HP_0029.
GeneIDi13869205.
899125.
KEGGiheo:C694_00135.
hpy:HP0029.
PATRICi20591257. VBIHelPyl33062_0030.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE000511 Genomic DNA. Translation: AAD07100.1 .
PIRi E64523.
RefSeqi NP_206831.1. NC_000915.1.
YP_006933951.1. NC_018939.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali O24872.
SMRi O24872. Positions 1-218.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

MINTi MINT-8303355.
STRINGi 85962.HP0029.

Proteomic databases

PRIDEi O24872.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAD07100 ; AAD07100 ; HP_0029 .
GeneIDi 13869205.
899125.
KEGGi heo:C694_00135.
hpy:HP0029.
PATRICi 20591257. VBIHelPyl33062_0030.

Phylogenomic databases

eggNOGi COG0132.
KOi K01935.
OMAi EENMLDF.
OrthoDBi EOG66B3XT.

Enzyme and pathway databases

UniPathwayi UPA00078 ; UER00161 .
BioCyci HPY:HP0029-MONOMER.

Miscellaneous databases

EvolutionaryTracei O24872.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
HAMAPi MF_00336. BioD.
InterProi IPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view ]
PIRSFi PIRSF006755. DTB_synth. 1 hit.
SUPFAMi SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR00347. bioD. 1 hit.
ProtoNeti Search...

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: September 3, 2014
This is version 89 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

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