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Information on EC 6.3.4.15 - biotin-[biotin carboxyl-carrier protein] ligase and Organism(s) Mycobacterium tuberculosis and UniProt Accession I6YFP0
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6.3.4.15 biotin-[biotin carboxyl-carrier protein] ligaseIUBMB Comments
The enzyme biotinylates a biotin carboxyl-carrier protein that is part of an acetyl-CoA carboxylase complex, enabling its subsequent carboxylation by EC 6.3.4.14, biotin carboxylase. The carboxyl group is eventually transferred to acetyl-CoA by EC 2.1.3.15, acetyl-CoA carboxytransferase. In some organisms the carrier protein is part of EC 6.4.1.2, acetyl-CoA carboxylase.
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Word Map
- 6.3.4.15
-
biotinylation
- streptavidin
-
bioid
-
proximity-dependent
- bap
- avidin
-
avitag
-
streptavidin-coated
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biotin-dependent
- transcarboxylase
-
proximity-labeling
-
biotinyl-5\'-amp
- drug development
-
unbiotinylated
-
15-amino
-
biotin-streptavidin
- diagnostics
- analysis
- synthesis
- carboxylases
The taxonomic range for the selected organisms is: Mycobacterium tuberculosis
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
Synonyms
biotin ligase, bira protein, biotin-protein ligase, biotin holoenzyme synthetase, bacterial bira biotin ligase, biotin acetyl-coa carboxylase ligase, group i biotin protein ligase, biotin:apocarboxylase ligase, holocarboxylase synthetase 1, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Acetyl CoA holocarboxylase synthetase
-
-
-
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Acetyl coenzyme A holocarboxylase synthetase
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-
-
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Biotin holoenzyme synthetase
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-
-
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Biotin--protein ligase
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-
-
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Biotin-[acetyl coenzyme A carboxylase] synthetase
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-
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Biotin-[acetyl-CoA carboxylase] synthetase
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-
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Biotin:apocarboxylase ligase
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-
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BirA
HCS
-
-
-
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Synthetase, biotin-[acetyl coenzyme A carboxylase]
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-
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additional information
additional information
-
the BPL of Mycobacterium tuberculosis belongs to the group I enzymes, monofunctional enzymes lacking the N-terminal HTH domain
additional information
the enzyme belongs to the biotin-dependent acetyl-CoA carboxylases/transcarboxylases
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
amination
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
biotin:apo-[carboxyl-carrier protein] ligase (AMP-forming)
The enzyme biotinylates a biotin carboxyl-carrier protein that is part of an acetyl-CoA carboxylase complex, enabling its subsequent carboxylation by EC 6.3.4.14, biotin carboxylase. The carboxyl group is eventually transferred to acetyl-CoA by EC 2.1.3.15, acetyl-CoA carboxytransferase. In some organisms the carrier protein is part of EC 6.4.1.2, acetyl-CoA carboxylase.
CAS REGISTRY NUMBER
COMMENTARY
37340-95-7
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + biotin + apo-[acetyl-CoA carbon-dioxide ligase]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase]
-
-
-
?
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
ATP + biotin + C-terminal domain of apo-biotin carboxyl carrier protein
AMP + diphosphate + biotinylated C-terminal domain of apo-biotin carboxyl carrier protein
Mycobacterium tuberculosis BPL specifically biotinylates the homologous BCCP domain BCCP87, but not the Escherichia coli domain BCCP87
-
-
?
biotin + ATP
biotinyl-5'-AMP + diphosphate
-
first half-reaction of BPL
-
-
?
D-biotin + ATP
biotinyl-5'-AMP + diphosphate
-
first half-reaction of BPL
-
-
?
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
-
-
-
?
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
-
overall reaction
-
-
?
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
-
overall reaction, BPL catalyses transfer of biotin to an epsilon-amino group of a specific lysine residue, which is usually the 35th amino acid from C-terminal of apoBCCP and converts it to active holoBCCP which promotes fatty acid initiation and elongation
-
-
?
biotinyl-5'-AMP + apocarboxylase
holocarboxylase + AMP
-
second half-reaction of BPL, the apocarboxylase is the biotin-carboxyl-carrier protein, which is carboxylated after biotin binding by the biotin carboxylase, BCCP, EC 6.3.4.14
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-
?
biotinyl-5'-AMP + apocarboxylase
holocarboxylase + AMP
-
second half-reaction of BPL, the apocarboxylase is the biotin-carboxyl-carrier protein, which is carboxylated after biotin binding by the biotin carboxylase, EC 6.3.4.14
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-
?
additional information
?
-
biotin-dependent acetyl-CoA carboxylases/transcarboxylases are a class of enzymes that, in addition to fatty-acid biosynthesis, are important for gluconeogenesis as well as propionate catabolism
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-
?
additional information
?
-
-
biotin-dependent acetyl-CoA carboxylases/transcarboxylases are a class of enzymes that, in addition to fatty-acid biosynthesis, are important for gluconeogenesis as well as propionate catabolism
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-
?
additional information
?
-
enzyme is not able to biotinylate Schatz' minimal peptide GLNDIFEAQKIEWH
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
biotin + ATP
biotinyl-5'-AMP + diphosphate
-
first half-reaction of BPL
-
-
?
biotinyl-5'-AMP + apocarboxylase
holocarboxylase + AMP
-
second half-reaction of BPL, the apocarboxylase is the biotin-carboxyl-carrier protein, which is carboxylated after biotin binding by the biotin carboxylase, BCCP, EC 6.3.4.14
-
-
?
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
-
-
-
?
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
-
overall reaction, BPL catalyses transfer of biotin to an epsilon-amino group of a specific lysine residue, which is usually the 35th amino acid from C-terminal of apoBCCP and converts it to active holoBCCP which promotes fatty acid initiation and elongation
-
-
?
additional information
?
-
biotin-dependent acetyl-CoA carboxylases/transcarboxylases are a class of enzymes that, in addition to fatty-acid biosynthesis, are important for gluconeogenesis as well as propionate catabolism
-
-
?
additional information
?
-
-
biotin-dependent acetyl-CoA carboxylases/transcarboxylases are a class of enzymes that, in addition to fatty-acid biosynthesis, are important for gluconeogenesis as well as propionate catabolism
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
biotin
-
dependent on, association of biotin and BPL is stabilized by 52 interactions, overview
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(2'R,6'S)-9-[6'-([[N-(D-biotinoyl)sulfamoyl]oxy]methyl)morpholin-2'-yl]adenine
nucleoside-based inhibitor, KD value 0.324 nM
2'-amino-5'-[N-(D-biotinoyl)sulfamoyl]amino-3',5'-dideoxyadenosine
nucleoside-based inhibitor, KD value 0.627 nM
9-[2'-azido-5'-O-[N-(D-biotinoyl)sulfamoyl]-2'-deoxy-beta-D-arabinofuranosyl]adenine
nucleoside-based inhibitor, KD value 0.027 nM. Strongest binding inhibitor in series
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0052
apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
-
pH 8.0, 37°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
holo-BPL is protected from proteolysis by biotinyl-5'-AMP, an intermediate of the BPL-catalyzed reaction. Apo-MtBPL is completely digested by trypsin within 20 min of co-ncubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of Mycobacterium tuberculosis BPL
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
BPL forms a weak dimer with bio-5'-AMP synthesized from ATP and biotin, on catalysis BPL forms monomeric and a weakly formed physiological dimer, both of which are holoenzymes
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structures of the apo-form and in complex with reaction intermediate biotinyl-5'-AMP. Binding of the reaction intermediate leads to clear disorder-to-order transitions. A conserved lysine, Lys138, in the active site is essential for biotinylation
purified recombinant enzyme, 0.003 ml of 5 mg/ml protein in 2.5 mM desthiobiotin in 20 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM PMSF and 1 mM DTT, is mixed with 0.003 ml of reservoir solution containing 12-16% w/v of both PEG 4000 and PEG 8000 in 0.1 M HEPES, pH 7.5, X-ray diffraction structure determination and analysis at 2.8 A resolution
structures of dehydrated and hydrated BirA, at 2.69 A and 2.8 A resolution, respectively. Dehydration of BirA crystals traps both the apo and active conformations in its asymmetric unit. The crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensues structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration results in a shift of 3.5 A in the flexible loop L6, a proline-rich loop unique to Mycobacterium tuberculosis complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein domain of ACCA3. The two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
R69A
the binding constant for biotin is nearly the same as that observed for the wild type protein. Mutant does not undergo self-botinylation
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
55
melting temperature, BirA-GFP fusion protein. Enzyme is not able to refold after the first cycle of heat denaturation
61
melting temperature, BirA-GFP fusion protein, presence of 1 mM biotin
71
melting temperature, BirA-GFP fusion protein, presence of both 1 mM biotin and 1 mM ATP
additional information
melting temperature does not change significantly in presence of ATP, GTP, CTP or UTP
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally Strep-tagged BirA from Escherichia coli
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene Rv3279c, DNA and amino acid sequence determination and analysis, expression of C-terminally Strep-tagged BirA in Escherichia coli
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
development of a high-throughput assay building on the principle of differential scanning fluorimetry of GFP-tagged proteins
drug development
drug development
-
the enzyme is a potential target for anti-mycobacterial drugs
drug development
the enzyme is a target for the design of effective antitubercular drugs
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bennett, C.B.; Westmoreland, T.J.; Verrier, C.S.; Blanchette, C.A.; Sabin, T.L.; Phatnani, H.P.; Mishina, Y.V.; Huper, G.; Selim, A.L.; Madison, E.R.; Bailey, D.D.; Falae, A.I.; Galli, A.; Olson, J.A.; Greenleaf, A.L.; Marks, J.R.
Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction
PLoS ONE
3
e1448
2008
Mycobacterium tuberculosis
Gupta, V.; Gupta, R.K.; Khare, G.; Surolia, A.; Salunke, D.M.; Tyagi, A.K.
Crystallization and preliminary X-ray diffraction analysis of biotin acetyl-CoA carboxylase ligase (BirA) from Mycobacterium tuberculosis
Acta Crystallogr. Sect. F
64
524-527
2008
Mycobacterium tuberculosis (P96884), Mycobacterium tuberculosis
Gupta, V.; Gupta, R.; Khare, G.; Salunke, D.; Surolia, A.; Tyagi, A.
Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration
PLoS ONE
5
e9222
2010
Mycobacterium tuberculosis (P96884), Mycobacterium tuberculosis
Purushothaman, S.; Annamalai, K.; Tyagi, A.; Surolia, A.
Diversity in functional organization of class I and class II biotin protein ligase
PLoS ONE
6
e16850
2011
Escherichia coli, Mycobacterium tuberculosis (P96884)
Bockman, M.R.; Kalinda, A.S.; Petrelli, R.; De la Mora-Rey, T.; Tiwari, D.; Liu, F.; Dawadi, S.; Nandakumar, M.; Rhee, K.Y.; Schnappinger, D.; Finzel, B.C.; Aldrich, C.C.
Targeting Mycobacterium tuberculosis biotin protein ligase (MtBPL) with nucleoside-based bisubstrate adenylation inhibitors
J. Med. Chem.
58
7349-7369
2015
Mycobacterium tuberculosis (I6YFP0), Mycobacterium tuberculosis H37Rv (I6YFP0)
Bond, T.E.H.; Sorenson, A.E.; Schaeffer, P.M.
A green fluorescent protein-based assay for high-throughput ligand-binding studies of a mycobacterial biotin protein ligase
Microbiol. Res.
205
35-39
2017
Mycobacterium tuberculosis (P96884), Mycobacterium tuberculosis CDC 1551 (P96884)
Ma, Q.; Akhter, Y.; Wilmanns, M.; Ehebauer, M.T.
Active site conformational changes upon reaction intermediate biotinyl-5-AMP binding in biotin protein ligase from Mycobacterium tuberculosis
Protein Sci.
23
932-939
2014
Mycobacterium tuberculosis (I6YFP0), Mycobacterium tuberculosis H37Rv (I6YFP0)
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