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Protein

ATP-dependent dethiobiotin synthetase BioD 1

Gene

bioD1

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.2 Publications

Catalytic activityi

ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin.1 Publication

Cofactori

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 1 (bioD1), ATP-dependent dethiobiotin synthetase BioD 2 (bioD2)
  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 bindingi13Magnesium 11
Metal bindingi17Magnesium 21
Binding sitei42Substrate1
Metal bindingi55Magnesium 21
Binding sitei55ATP1
Metal bindingi116Magnesium 21
Binding sitei212ATP1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi13 – 18ATP6
Nucleotide bindingi116 – 119ATP4
Nucleotide bindingi176 – 177ATP2
Nucleotide bindingi205 – 207ATP3

GO - Molecular functioni

  • ATP binding Source: UniProtKB
  • dethiobiotin synthase activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB

GO - Biological processi

  • biotin biosynthetic process Source: UniProtKB
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

BioCyciEcoCyc:DETHIOBIOTIN-SYN-MONOMER.
ECOL316407:JW0761-MONOMER.
MetaCyc:DETHIOBIOTIN-SYN-MONOMER.
SABIO-RKP13000.
UniPathwayiUPA00078; UER00161.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent dethiobiotin synthetase BioD 1 (EC:6.3.3.3)
Alternative name(s):
DTB synthetase 1
Short name:
DTBS 1
Dethiobiotin synthase
Gene namesi
Name:bioD1
Ordered Locus Names:b0778, JW0761
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10120. bioD1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi12T → V: Strong decreased in the affinity for ATP; essential role for this residue in the steady-state affinity for ATP. 1 Publication1
Mutagenesisi13E → A or D: Almost no change in activity. 1 Publication1
Mutagenesisi16K → Q: Complete loss of activity. 1 Publication1
Mutagenesisi38K → L, Q or R: Complete loss of activity. 1 Publication1
Mutagenesisi42S → A or C: Almost no change in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001879612 – 225ATP-dependent dethiobiotin synthetase BioD 1Add BLAST224

Proteomic databases

PaxDbiP13000.
PRIDEiP13000.

Interactioni

Subunit structurei

Homodimer.6 Publications

Protein-protein interaction databases

BioGridi4259956. 11 interactors.
IntActiP13000. 3 interactors.
STRINGi511145.b0778.

Structurei

Secondary structure

1225
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 11Combined sources9
Helixi16 – 29Combined sources14
Beta strandi34 – 37Combined sources4
Beta strandi39 – 43Combined sources5
Beta strandi45 – 47Combined sources3
Beta strandi50 – 52Combined sources3
Helixi54 – 61Combined sources8
Beta strandi63 – 65Combined sources3
Helixi69 – 72Combined sources4
Beta strandi74 – 79Combined sources6
Helixi83 – 90Combined sources8
Helixi96 – 107Combined sources12
Beta strandi111 – 116Combined sources6
Beta strandi118 – 120Combined sources3
Beta strandi124 – 126Combined sources3
Helixi131 – 138Combined sources8
Beta strandi142 – 147Combined sources6
Helixi152 – 165Combined sources14
Beta strandi170 – 176Combined sources7
Helixi185 – 195Combined sources11
Beta strandi196 – 198Combined sources3
Beta strandi200 – 204Combined sources5
Turni211 – 213Combined sources3
Helixi217 – 219Combined sources3
Helixi222 – 224Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A82X-ray1.80A2-225[»]
1BS1X-ray1.80A2-225[»]
1BYIX-ray0.97A2-225[»]
1DADX-ray1.60A2-225[»]
1DAEX-ray1.70A2-225[»]
1DAFX-ray1.70A2-225[»]
1DAGX-ray1.64A2-225[»]
1DAHX-ray1.64A2-225[»]
1DAIX-ray1.64A2-225[»]
1DAKX-ray1.60A2-225[»]
1DAMX-ray1.80A2-225[»]
1DBSX-ray1.80A2-225[»]
1DTSX-ray1.65A1-224[»]
ProteinModelPortaliP13000.
SMRiP13000.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13000.

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.Curated

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
InParanoidiP13000.
KOiK01935.
OMAiCINHAVL.
PhylomeDBiP13000.

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]
PIRSFiPIRSF006755. DTB_synth. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00347. bioD. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P13000-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKRYFVTGT DTEVGKTVAS CALLQAAKAA GYRTAGYKPV ASGSEKTPEG
60 70 80 90 100
LRNSDALALQ RNSSLQLDYA TVNPYTFAEP TSPHIISAQE GRPIESLVMS
110 120 130 140 150
AGLRALEQQA DWVLVEGAGG WFTPLSDTFT FADWVTQEQL PVILVVGVKL
160 170 180 190 200
GCINHAMLTA QVIQHAGLTL AGWVANDVTP PGKRHAEYMT TLTRMIPAPL
210 220
LGEIPWLAEN PENAATGKYI NLALL
Length:225
Mass (Da):24,140
Last modified:January 23, 2007 - v3
Checksum:i9AE76F3BE6565780
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti29A → R in AAA23518 (PubMed:3058702).Curated1
Sequence conflicti108 – 109QQ → HK in CAA00967 (Ref. 3) Curated2
Sequence conflicti198 – 225APLLG…NLALL → RRCWERSPGLQKIQKMRQPE ST in AAA23518 (PubMed:3058702).CuratedAdd BLAST28

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04423 Genomic DNA. Translation: AAA23518.1.
S68059 Genomic DNA. Translation: AAB29683.2.
A11538 Unassigned DNA. Translation: CAA00967.1.
U00096 Genomic DNA. Translation: AAC73865.1.
AP009048 Genomic DNA. Translation: BAE76365.1.
PIRiB64814. SYECDB.
RefSeqiNP_415299.1. NC_000913.3.
WP_000044843.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73865; AAC73865; b0778.
BAE76365; BAE76365; BAE76365.
GeneIDi945387.
KEGGiecj:JW0761.
eco:b0778.
PATRICi32116757. VBIEscCol129921_0804.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04423 Genomic DNA. Translation: AAA23518.1.
S68059 Genomic DNA. Translation: AAB29683.2.
A11538 Unassigned DNA. Translation: CAA00967.1.
U00096 Genomic DNA. Translation: AAC73865.1.
AP009048 Genomic DNA. Translation: BAE76365.1.
PIRiB64814. SYECDB.
RefSeqiNP_415299.1. NC_000913.3.
WP_000044843.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A82X-ray1.80A2-225[»]
1BS1X-ray1.80A2-225[»]
1BYIX-ray0.97A2-225[»]
1DADX-ray1.60A2-225[»]
1DAEX-ray1.70A2-225[»]
1DAFX-ray1.70A2-225[»]
1DAGX-ray1.64A2-225[»]
1DAHX-ray1.64A2-225[»]
1DAIX-ray1.64A2-225[»]
1DAKX-ray1.60A2-225[»]
1DAMX-ray1.80A2-225[»]
1DBSX-ray1.80A2-225[»]
1DTSX-ray1.65A1-224[»]
ProteinModelPortaliP13000.
SMRiP13000.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259956. 11 interactors.
IntActiP13000. 3 interactors.
STRINGi511145.b0778.

Proteomic databases

PaxDbiP13000.
PRIDEiP13000.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73865; AAC73865; b0778.
BAE76365; BAE76365; BAE76365.
GeneIDi945387.
KEGGiecj:JW0761.
eco:b0778.
PATRICi32116757. VBIEscCol129921_0804.

Organism-specific databases

EchoBASEiEB0118.
EcoGeneiEG10120. bioD1.

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
InParanoidiP13000.
KOiK01935.
OMAiCINHAVL.
PhylomeDBiP13000.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciEcoCyc:DETHIOBIOTIN-SYN-MONOMER.
ECOL316407:JW0761-MONOMER.
MetaCyc:DETHIOBIOTIN-SYN-MONOMER.
SABIO-RKP13000.

Miscellaneous databases

EvolutionaryTraceiP13000.
PROiP13000.

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]
PIRSFiPIRSF006755. DTB_synth. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00347. bioD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiBIOD1_ECOLI
AccessioniPrimary (citable) accession number: P13000
Secondary accession number(s): Q2MBJ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 149 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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.