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Escherichia coli K-12 substr. MG1655 Enzyme: dethiobiotin synthetase



Gene: bioD Accession Numbers: EG10120 (EcoCyc), b0778, ECK0767

Regulation Summary Diagram: ?

Subunit composition of dethiobiotin synthetase = [BioD]2
         dethiobiotin synthetase monomer = BioD

Summary:
Dethiobiotin synthetase catalyzes the first ring closure in the biosynthesis of biotin, which is the penultimate step in the biosynthesis pathway. It is a functionally unique enzyme which catalyzes a carboxylation reaction that does not require biotin as a prosthetic group [Krell70].

The active form of the enzyme is a homodimer [Huang95a, Alexeev95].

Crystal structures of dethiobiotin synthetase alone and in various binary, ternary and quarternary complexes have been solved [Alexeev94, Huang94b, Alexeev94a, Huang95a, Kack98, Sandalova99]. A reaction mechanism has been proposed [Huang95a]. The carboxylation site is the N7 amino group of 7,8-diaminopelargonate [Alexeev95]. Site-directed mutagenesis of active site residues provided further insight into the catalytic mechanism [Yang97b]. The mixed carbamic phosphoric anhydride intermediate of the reaction has been isolated and observed by kinetic crystallography [Gibson97b, Kack98a].

Review: [Schneider97b]

Gene Citations: [Nath82]

Locations: cytosol

Map Position: [811,493 -> 812,170] (17.49 centisomes)
Length: 678 bp / 225 aa

Molecular Weight of Polypeptide: 24.14 kD (from nucleotide sequence), 24.5 kD (experimental) [Krell70 ]

Molecular Weight of Multimer: 42 kD (experimental) [Krell70]

pI: 8.88

Unification Links: ASAP:ABE-0002650 , CGSC:956 , EchoBASE:EB0118 , EcoGene:EG10120 , EcoliWiki:b0778 , ModBase:P13000 , OU-Microarray:b0778 , PortEco:bioD , PR:PRO_000022224 , Pride:P13000 , Protein Model Portal:P13000 , RefSeq:NP_415299 , RegulonDB:EG10120 , SMR:P13000 , String:511145.b0778 , UniProt:P13000

Relationship Links: InterPro:IN-FAMILY:IPR002586 , InterPro:IN-FAMILY:IPR004472 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:1A82 , PDB:Structure:1BS1 , PDB:Structure:1BYI , PDB:Structure:1DAD , PDB:Structure:1DAE , PDB:Structure:1DAF , PDB:Structure:1DAG , PDB:Structure:1DAH , PDB:Structure:1DAI , PDB:Structure:1DAK , PDB:Structure:1DAM , PDB:Structure:1DBS , PDB:Structure:1DTS , Pfam:IN-FAMILY:PF01656

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009102 - biotin biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Eisenberg69, Rolfe70]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Huang95a]
GO:0004141 - dethiobiotin synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Krell70, Gibson95a]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Huang95a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers biotin

Essentiality data for bioD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 5]

Credits:
Last-Curated ? 16-Jan-2007 by Keseler I , SRI International


Enzymatic reaction of: dethiobiotin synthetase

Synonyms: DTBS, DTB synthetase, 7,8-diaminononanoate: carbon-dioxide cyclo-ligase (ADP-forming)

EC Number: 6.3.3.3

CO2 + 7,8-diaminopelargonate + ATP <=> dethiobiotin + ADP + phosphate + 3 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for 7,8-diaminopelargonate: diaminobiotin [Krell70 ]

Alternative Substrates for ATP: CTP [Comment 6 , Krell70 ]

In Pathways: biotin biosynthesis I , biotin biosynthesis from 8-amino-7-oxononanoate I

Cofactors or Prosthetic Groups: Mg2+ [Comment 7, Alexeev95, Krell70]

Inhibitors (Competitive): ADP [Krell70, Comment 8]

Kinetic Parameters:

Substrate
Km (μM)
Citations
7,8-diaminopelargonate
1.3
[Eisenberg79, BRENDA14]
7,8-diaminopelargonate
0.3
[Gibson95a]
ATP
5.0
[Eisenberg79, BRENDA14]
ATP
0.4
[Gibson95a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Alexeev94, UniProt11]
UniProt: Removed.
Chain 2 -> 225
[UniProt09]
UniProt: Dethiobiotin synthetase;
Mutagenesis-Variant 12
[Yang97b, UniProt11a]
Alternate sequence: T → V; UniProt: Strong decreased in the affinity for ATP; essential role for this residue in the steady-state affinity for ATP.
Mutagenesis-Variant 13
[Yang97b, UniProt11a]
Alternate sequence: E → D; UniProt: Almost no change in activity.
Alternate sequence: E → A; UniProt: Almost no change in activity.
Metal-Binding-Site 13
[UniProt11]
UniProt: Magnesium 1.
Nucleotide-Phosphate-Binding-Region 13 -> 18
[UniProt11]
UniProt: ATP.
Mutagenesis-Variant 16
[Yang97b, UniProt11a]
Alternate sequence: K → Q; UniProt: Complete loss of activity.
Metal-Binding-Site 17
[UniProt11]
UniProt: Magnesium 2.
Sequence-Conflict 29
[Otsuka88, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1; AAA23518);
Mutagenesis-Variant 38
[Yang97b, UniProt11a]
Alternate sequence: K → R; UniProt: Complete loss of activity.
Alternate sequence: K → Q; UniProt: Complete loss of activity.
Alternate sequence: K → L; UniProt: Complete loss of activity.
Mutagenesis-Variant 42
[Yang97b, UniProt11a]
Alternate sequence: S → C; UniProt: Almost no change in activity.
Alternate sequence: S → A; UniProt: Almost no change in activity.
Amino-Acid-Sites-That-Bind 42
[UniProt11]
UniProt: Substrate.
Metal-Binding-Site 55
[UniProt11]
UniProt: Magnesium 2.
Sequence-Conflict 108 -> 109
[UniProt10b]
Alternate sequence: QQ → HK; UniProt: (in Ref. 3; CAA00967);
Metal-Binding-Site 116
[UniProt11]
UniProt: Magnesium 2.
Nucleotide-Phosphate-Binding-Region 116 -> 119
[UniProt11]
UniProt: ATP.
Nucleotide-Phosphate-Binding-Region 176 -> 177
[UniProt11]
UniProt: ATP.
Sequence-Conflict 198 -> 225
[Otsuka88, UniProt10]
Alternate sequence: APLLGEIPWLAENPENAATGKYINLALL → RRCWERSPGLQKIQKMRQPEST; UniProt: (in Ref. 1; AAA23518);
Nucleotide-Phosphate-Binding-Region 205 -> 207
[UniProt11]
UniProt: ATP.
Amino-Acid-Sites-That-Bind 212
[UniProt11]
UniProt: ATP.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0778 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10120; confirmed by SwissProt match.


References

Alexeev94: Alexeev D, Bury SM, Boys CW, Turner MA, Sawyer L, Ramsey AJ, Baxter HC, Baxter RL (1994). "Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis." J Mol Biol 1994;235(2);774-6. PMID: 8289297

Alexeev94a: Alexeev D, Baxter RL, Sawyer L (1994). "Mechanistic implications and family relationships from the structure of dethiobiotin synthetase." Structure 2(11);1061-72. PMID: 7881906

Alexeev95: Alexeev D, Baxter RL, Smekal O, Sawyer L (1995). "Substrate binding and carboxylation by dethiobiotin synthetase--a kinetic and X-ray study." Structure 3(11);1207-15. PMID: 8591031

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Baxter94: Baxter RL, Ramsey AJ, McIver LA, Baxter HC (1994). "Mechanism of Dethiobiotin Synthetase -- Characterisation of the 8-Aminocarbamate of (7R,8S)-7,8 Diaminononanoate as an Enzyme-bound Intermediate." J Chem Soc Chem Comm (1994);559-560.

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Eisenberg69: Eisenberg MA, Krell K (1969). "Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12." J Bacteriol 98(3);1227-31. PMID: 4892372

Eisenberg79: Eisenberg MA, Krell K (1979). "Dethiobiotin synthetase." Methods Enzymol 62;348-52. PMID: 374977

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gibson95a: Gibson KJ, Lorimer GH, Rendina AR, Taylor WS, Cohen G, Gatenby AA, Payne WG, Roe DC, Lockett BA, Nudelman A (1995). "Dethiobiotin synthetase: the carbonylation of 7,8-diaminonanoic acid proceeds regiospecifically via the N7-carbamate." Biochemistry 34(35);10976-84. PMID: 7669755

Gibson97b: Gibson KJ (1997). "Isolation and chemistry of the mixed anhydride intermediate in the reaction catalyzed by dethiobiotin synthetase." Biochemistry 36(28);8474-8. PMID: 9214291

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Huang94b: Huang W, Lindqvist Y, Schneider G, Gibson KJ, Flint D, Lorimer G (1994). "Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution." Structure 2(5);407-14. PMID: 8081756

Huang95a: Huang W, Jia J, Gibson KJ, Taylor WS, Rendina AR, Schneider G, Lindqvist Y (1995). "Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate." Biochemistry 34(35);10985-95. PMID: 7669756

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kack98: Kack H, Sandmark J, Gibson KJ, Schneider G, Lindqvist Y (1998). "Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis." Protein Sci 7(12);2560-6. PMID: 9865950

Kack98a: Kack H, Gibson KJ, Lindqvist Y, Schneider G (1998). "Snapshot of a phosphorylated substrate intermediate by kinetic crystallography." Proc Natl Acad Sci U S A 95(10);5495-500. PMID: 9576910

Krell70: Krell K, Eisenberg MA (1970). "The purification and properties of dethiobiotin synthetase." J Biol Chem 1970;245(24);6558-66. PMID: 4921568

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Nath82: Nath SK, Guha A (1982). "Abortive termination of bioBFCD RNA synthesized in vitro from the bioABFCD operon of Escherichia coli K-12." Proc Natl Acad Sci U S A 79(6);1786-90. PMID: 6177001

Otsuka88: Otsuka AJ, Buoncristiani MR, Howard PK, Flamm J, Johnson C, Yamamoto R, Uchida K, Cook C, Ruppert J, Matsuzaki J (1988). "The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon." J Biol Chem 263(36);19577-85. PMID: 3058702

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Rolfe70: Rolfe B (1970). "Lambda phage transduction of the bio A locus of Escherichia coli." Virology 42(3);643-61. PMID: 4921685

Sandalova99: Sandalova T, Schneider G, Kack H, Lindqvist Y (1999). "Structure of dethiobiotin synthetase at 0.97 A resolution." Acta Crystallogr D Biol Crystallogr 55(Pt 3);610-24. PMID: 10089457

Schneider97b: Schneider G, Lindqvist Y (1997). "Structure of ATP-dependent carboxylase, dethiobiotin synthase." Methods Enzymol 279;376-85. PMID: 9211290

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Yang97b: Yang G, Sandalova T, Lohman K, Lindqvist Y, Rendina AR (1997). "Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties." Biochemistry 36(16);4751-60. PMID: 9125495

Other References Related to Gene Regulation

AbdelHamid07: Abdel-Hamid AM, Cronan JE (2007). "Coordinate expression of the acetyl coenzyme A carboxylase genes, accB and accC, is necessary for normal regulation of biotin synthesis in Escherichia coli." J Bacteriol 189(2);369-76. PMID: 17056747

Cronan89: Cronan JE (1989). "The E. coli bio operon: transcriptional repression by an essential protein modification enzyme." Cell 58(3);427-9. PMID: 2667763

Lin91a: Lin KC, Campbell A, Shiuan D (1991). "Binding characteristics of Escherichia coli biotin repressor-operator complex." Biochim Biophys Acta 1090(3);317-25. PMID: 1659455

Otsuka78: Otsuka A, Abelson J (1978). "The regulatory region of the biotin operon in Escherichia coli." Nature 1978;276(5689);689-94. PMID: 366433


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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