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P13000

- BIOD1_ECOLI

UniProt

P13000 - BIOD1_ECOLI

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Protein

ATP-dependent dethiobiotin synthetase BioD 1

Gene

bioD1

Organism
Escherichia coli (strain K12)
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. 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi13 – 131Magnesium 1
Metal bindingi17 – 171Magnesium 2
Binding sitei42 – 421Substrate
Metal bindingi55 – 551Magnesium 2
Binding sitei55 – 551ATP
Metal bindingi116 – 1161Magnesium 2
Binding sitei212 – 2121ATP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi13 – 186ATP
Nucleotide bindingi116 – 1194ATP
Nucleotide bindingi176 – 1772ATP
Nucleotide bindingi205 – 2073ATP

GO - Molecular functioni

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

GO - Biological processi

  1. 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10120. bioD1.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi12 – 121T → V: Strong decreased in the affinity for ATP; essential role for this residue in the steady-state affinity for ATP. 1 Publication
Mutagenesisi13 – 131E → A or D: Almost no change in activity. 1 Publication
Mutagenesisi16 – 161K → Q: Complete loss of activity. 1 Publication
Mutagenesisi38 – 381K → L, Q or R: Complete loss of activity. 1 Publication
Mutagenesisi42 – 421S → A or C: Almost no change in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 225224ATP-dependent dethiobiotin synthetase BioD 1PRO_0000187961Add
BLAST

Proteomic databases

PaxDbiP13000.
PRIDEiP13000.

Expressioni

Gene expression databases

GenevestigatoriP13000.

Interactioni

Subunit structurei

Homodimer.6 Publications

Protein-protein interaction databases

IntActiP13000. 3 interactions.
STRINGi511145.b0778.

Structurei

Secondary structure

1
225
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Helixi16 – 2914Combined sources
Beta strandi34 – 374Combined sources
Beta strandi39 – 435Combined sources
Beta strandi45 – 473Combined sources
Beta strandi50 – 523Combined sources
Helixi54 – 618Combined sources
Beta strandi63 – 653Combined sources
Helixi69 – 724Combined sources
Beta strandi74 – 796Combined sources
Helixi83 – 908Combined sources
Helixi96 – 10712Combined sources
Beta strandi111 – 1166Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi124 – 1263Combined sources
Helixi131 – 1388Combined sources
Beta strandi142 – 1476Combined sources
Helixi152 – 16514Combined sources
Beta strandi170 – 1767Combined sources
Helixi185 – 19511Combined sources
Beta strandi196 – 1983Combined sources
Beta strandi200 – 2045Combined sources
Turni211 – 2133Combined sources
Helixi217 – 2193Combined sources
Helixi222 – 2243Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-225.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13000.

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.Curated

Phylogenomic databases

eggNOGiCOG0132.
HOGENOMiHOG000275032.
InParanoidiP13000.
KOiK01935.
OMAiCINHAVL.
OrthoDBiEOG66B3XT.
PhylomeDBiP13000.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD.
InterProiIPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
IPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF01656. CbiA. 1 hit.
[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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti29 – 291A → R in AAA23518. (PubMed:3058702)Curated
Sequence conflicti108 – 1092QQ → HK in CAA00967. 1 PublicationCurated
Sequence conflicti198 – 22528APLLG…NLALL → RRCWERSPGLQKIQKMRQPE ST in AAA23518. (PubMed:3058702)CuratedAdd
BLAST

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.
YP_489051.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73865; AAC73865; b0778.
BAE76365; BAE76365; BAE76365.
GeneIDi12930962.
945387.
KEGGiecj:Y75_p0751.
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 .
PIRi B64814. SYECDB.
RefSeqi NP_415299.1. NC_000913.3.
YP_489051.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1A82 X-ray 1.80 A 2-225 [» ]
1BS1 X-ray 1.80 A 2-225 [» ]
1BYI X-ray 0.97 A 2-225 [» ]
1DAD X-ray 1.60 A 2-225 [» ]
1DAE X-ray 1.70 A 2-225 [» ]
1DAF X-ray 1.70 A 2-225 [» ]
1DAG X-ray 1.64 A 2-225 [» ]
1DAH X-ray 1.64 A 2-225 [» ]
1DAI X-ray 1.64 A 2-225 [» ]
1DAK X-ray 1.60 A 2-225 [» ]
1DAM X-ray 1.80 A 2-225 [» ]
1DBS X-ray 1.80 A 2-225 [» ]
1DTS X-ray 1.65 A 1-224 [» ]
ProteinModelPortali P13000.
SMRi P13000. Positions 2-225.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P13000. 3 interactions.
STRINGi 511145.b0778.

Proteomic databases

PaxDbi P13000.
PRIDEi P13000.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73865 ; AAC73865 ; b0778 .
BAE76365 ; BAE76365 ; BAE76365 .
GeneIDi 12930962.
945387.
KEGGi ecj:Y75_p0751.
eco:b0778.
PATRICi 32116757. VBIEscCol129921_0804.

Organism-specific databases

EchoBASEi EB0118.
EcoGenei EG10120. bioD1.

Phylogenomic databases

eggNOGi COG0132.
HOGENOMi HOG000275032.
InParanoidi P13000.
KOi K01935.
OMAi CINHAVL.
OrthoDBi EOG66B3XT.
PhylomeDBi P13000.

Enzyme and pathway databases

UniPathwayi UPA00078 ; UER00161 .
BioCyci EcoCyc:DETHIOBIOTIN-SYN-MONOMER.
ECOL316407:JW0761-MONOMER.
MetaCyc:DETHIOBIOTIN-SYN-MONOMER.
SABIO-RK P13000.

Miscellaneous databases

EvolutionaryTracei P13000.
PROi P13000.

Gene expression databases

Genevestigatori P13000.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
HAMAPi MF_00336. BioD.
InterProi IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
IPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view ]
Pfami PF01656. CbiA. 1 hit.
[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. "The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon."
    Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.
    J. Biol. Chem. 263:19577-19585(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis."
    Alexeev D., Bury S.M., Boys C.W.G., Turner M.A., Sawyer L., Ramsey A.J., Baxter H.C., Baxter R.L.
    J. Mol. Biol. 235:774-776(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20 AND 224-225.
  3. "Genetic material for expression of biotin synthetase enzymes."
    Pearson B.M., McKee R.A.
    Patent number GB2216530, 11-OCT-1989
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12."
    Eisenberg M.A., Krell K.
    J. Bacteriol. 98:1227-1231(1969) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN BIOTIN BIOSYNTHESIS.
  7. "The purification and properties of dethiobiotin synthetase."
    Krell K., Eisenberg M.A.
    J. Biol. Chem. 245:6558-6566(1970) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DETHIOBIOTIN SYNTHETASE, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT.
  8. "Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties."
    Yang G., Sandalova T., Lohman K., Lindqvist Y., Rendina A.R.
    Biochemistry 36:4751-4760(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF THR-12; GLU-13; LYS-16; LYS-38 AND SER-42.
  9. "Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65-A resolution."
    Huang W., Lindqvist Y., Schneider G., Gibson K.J., Flint D., Lorimer G.
    Structure 2:407-414(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), SUBUNIT.
  10. "Mechanistic implications and family relationships from the structure of dethiobiotin synthetase."
    Sawyer L., Baxter R.L., Alexeev D.
    Structure 2:1061-1072(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, SUBUNIT.
  11. "Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate."
    Huang W., Jia J., Gibson K.J., Taylor W.S., Rendina A.R., Schneider G., Lindqvist Y.
    Biochemistry 34:10985-10995(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 2-224 IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, REACTION MECHANISM.
  12. "Snapshot of a phosphorylated substrate intermediate by kinetic crystallography."
    Kaeck H., Gibson K.J., Lindqvist Y., Schneider G.
    Proc. Natl. Acad. Sci. U.S.A. 95:5495-5500(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP, MAGNESIUM IONS.
  13. "Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis."
    Kaeck H., Sandmark J., Gibson K.J., Schneider G., Lindqvist Y.
    Protein Sci. 7:2560-2566(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ATP AND MAGNESIUM IONS, SUBUNIT.
  14. "Structure of dethiobiotin synthetase at 0.97-A resolution."
    Sandalova T., Schneider G., Kack H., Lindqvist Y.
    Acta Crystallogr. D 55:610-624(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS).

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 26, 2014
This is version 139 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

External Data

Dasty 3