PDBsum entry: 2v59

Ligase

PDB-id: 2v59

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PROCHECK

Protein chains

445 a.a.

Ligands

LZK ×2

Waters ×236

Tools

Clefts Calculation

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PDB id:

2v59

Name:

Ligase

Title:

Crystal structure of biotin carboxylase from e.Coli in complex with potent inhibitor 2

Structure:

Biotin carboxylase. Chain: a, b. Synonym: acetyl-coa carboxylase subunit a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

Chains A, B: P24182 (ACCC_ECOLI)

Seq:

Struc:

Seq:

449 a.a.

Struc:

445 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class 1:

E.C.6.3.4.14   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + biotin-carboxyl-carrier protein + CO₂ = ADP + phosphate + carboxybiotin-carboxyl-carrier protein (see diagram below)

Enzyme class 2:

E.C.6.4.1.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + acetyl-CoA + HCO₃^- = ADP + phosphate + malonyl-CoA (see diagram below)

Cofactor:

Biotin

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Resolution:

2.40Å

R-factor:

0.210

R-free:

0.248

Authors:

I.Mochalkin,J.R.Miller

Key ref:

J.R.Miller et al. (2009). A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore.. Proc Natl Acad Sci U S A, 106, 1737-1742. [PubMed id: 19164768] [DOI: 10.1073/pnas.0811275106]

Date:

02-Oct-08

Release date:

13-Jan-09

Related entries:

2j9g crystal structure of biotin carboxylase from e. Coli in complex with amppnp and adp
2vr1 crystal structure of biotin carboxylase from e. Coli in complex with atp analog, adpcf2p.
2gpw crystal structure of the biotin carboxylase subunit, f363amutant, of acetyl-coa carboxylase from escherichia coli.
1k69 model interaction between bccp and atp-bound carboxylasesubunit of acetyl coa carboxylase
1dv1 structure of biotin carboxylase (apo)
1bnc
2gps crystal structure of the biotin carboxylase subunit, e23rmutant, of acetyl-coa carboxylase from escherichia coli.
1dv2 the structure of biotin carboxylase, mutant e288k, complexed with atp
2v58 crystal structure of biotin carboxylase from e.Coli in complex with potent inhibitor 1
2v5a crystal structure of biotin carboxylase from e.Coli in complex with potent inhibitor 3

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Key reference

DOI no: 10.1073/pnas.0811275106

Proc Natl Acad Sci U S A 106:1737-1742 (2009)

PubMed id: 19164768

A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore.

J.R.Miller, S.Dunham, I.Mochalkin, C.Banotai, M.Bowman, S.Buist, B.Dunkle, D.Hanna, H.J.Harwood, M.D.Huband, A.Karnovsky, M.Kuhn, C.Limberakis, J.Y.Liu, S.Mehrens, W.T.Mueller, L.Narasimhan, A.Ogden, J.Ohren, J.V.Prasad, J.A.Shelly, L.Skerlos, M.Sulavik, V.H.Thomas, S.VanderRoest, L.Wang, Z.Wang, A.Whitton, T.Zhu, C.K.Stover.

ABSTRACT

As the need for novel antibiotic classes to combat bacterial drug resistance increases, the paucity of leads resulting from target-based antibacterial screening of pharmaceutical compound libraries is of major concern. One explanation for this lack of success is that antibacterial screening efforts have not leveraged the eukaryotic bias resulting from more extensive chemistry efforts targeting eukaryotic gene families such as G protein-coupled receptors and protein kinases. Consistent with a focus on antibacterial target space resembling these eukaryotic targets, we used whole-cell screening to identify a series of antibacterial pyridopyrimidines derived from a protein kinase inhibitor pharmacophore. In bacteria, the pyridopyrimidines target the ATP-binding site of biotin carboxylase (BC), which catalyzes the first enzymatic step of fatty acid biosynthesis. These inhibitors are effective in vitro and in vivo against fastidious gram-negative pathogens including Haemophilus influenzae. Although the BC active site has architectural similarity to those of eukaryotic protein kinases, inhibitor binding to the BC ATP-binding site is distinct from the protein kinase-binding mode, such that the inhibitors are selective for bacterial BC. In summary, we have discovered a promising class of potent antibacterials with a previously undescribed mechanism of action. In consideration of the eukaryotic bias of pharmaceutical libraries, our findings also suggest that pursuit of a novel inhibitor leads for antibacterial targets with active-site structural similarity to known human targets will likely be more fruitful than the traditional focus on unique bacterial target space, particularly when structure-based and computational methodologies are applied to ensure bacterial selectivity.

Selected figure(s)

Figure 1.
Pyridopyrimidine inhibitor structures and sites of resistance-conferring mutations in biotin carboxylase. (A) Pyridopyrimidine inhibitors of BC (1, 2, and 3) and FGFR1 (4). (B) X-ray costructure of ADP and E. coli BC (8). Residues conferring resistance to 1 upon mutation are highlighted.

Figure 2.
Binding modes of pyridopyrimidine inhibitors. (A) View of the unambiguous (F[o] − F[c]) OMIT electron density map of inhibitor 1 calculated by omitting 1 during simulated annealing. Map is superimposed on the final refined model and contoured at 2.5 σ level. Inhibitor 1 is shown in sticks with the following atom colors: carbon, green; nitrogen, blue; oxygen, red; and bromine, cherry red. Ribbon representation of BC is in green. (B) View of the superimposed ATP-binding site in complexes with inhibitor 1 and ADP [Protein Data Bank (PDB) ID code 2j9g]. Ribbon representation of the EcBC/inhibitor 1 coordinates is in green. Ribbon representation of the EcBC/ADP coordinates is in yellow. EcBC residues involved in interactions with ADP are shown in sticks with the following atom colors: carbon, yellow; nitrogen, blue; oxygen, red. (C) Overlay of compound 1 bound in the ATP-binding site of BC (green carbons) vs. compound 1 docked into the ATP-binding site of FGFR1 (PDB ID code 2fgi; cyan carbons). The conformation of ATP bound to both kinases is shown in gray as a guide. (D) View of the distinctively different binding modes of inhibitor 1 and compound 4 in the superimposed ATP-binding sites of BC and FGFR1 (PDB ID code 2fgi). Ribbon representation of the EcBC/inhibitor 1 coordinates is in green. Ribbon representation of the FGFR/compound 4 coordinates is in pink. Images were prepared by using PyMOL molecular graphics systems (DeLano Scientific LLC).

Figures were selected by an automated process.