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Protein

ATP-dependent dethiobiotin synthetase BioD 1

Gene

bioD1

Organism
Escherichia coli (strain K12)
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. 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

Keywordsi

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

Enzyme and pathway databases

BioCyciEcoCyc:DETHIOBIOTIN-SYN-MONOMER
MetaCyc:DETHIOBIOTIN-SYN-MONOMER
SABIO-RKiP13000
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

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

Chemistry databases

DrugBankiDB02941 3-(1-Aminoethyl)Nonanedioic Acid
DB03624 7-(Carboxyamino)-8-Amino-Nonanoic Acid
DB03775 D-Dethiobiotin

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, 20 interactors
IntActiP13000, 3 interactors
STRINGi316385.ECDH10B_0846

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
OMAiDYWKPIQ
PhylomeDBiP13000

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
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
PATRICifig|1411691.4.peg.1500

Similar proteinsi

Entry informationi

Entry nameiBIOD1_ECOLI
AccessioniPrimary (citable) accession number: P13000
Secondary accession number(s): Q2MBJ1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 156 of the entry and version 3 of the sequence. See 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

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