Catalytic mechanism and cofactor preference of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus

Dommaraju, Sudhir R.; Dogovski, Con; Czabotar, P.E.; Hor, Lilian; Smith, Brian J.; Perugini, Matthew A.

doi:10.1016/j.abb.2011.06.006

Cited by 20 publications

(19 citation statements)

References 40 publications

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“…HTPA is subsequently non-enzymatically dehydrated to dihydrodipicolinate (DHDP), which is then reduced by dihydrodipicolinate reductase (DHDPR) (EC1.17.1.8) to form tetrahydrodipicolinate (THDP) (Fig. 1A)11011. The pathway then diverges into four sub-pathways, namely the acetylase, aminotransferase, dehydrogenase and succinylase pathways, which operate across different genera and kingdoms21213.…”

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Structure and Function of Cyanobacterial DHDPS and DHDPR

Christensen

Costa

Faou

et al. 2016

Sci Rep

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Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase (DHDPS) followed by a reduction reaction catalysed by dihydrodipicolinate reductase (DHDPR). Interestingly, both DHDPS and DHDPR exist as different oligomeric forms in bacteria and plants. DHDPS is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. DHDPR also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of DHDPS and DHDPR from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified DHDPS and DHDPR from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative DHDPS-DHDPR coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of DHDPS and DHDPR from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant DHDPS and DHDPR diverged after cyanobacteria evolved.

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Structure and Function of Cyanobacterial DHDPS and DHDPR

Christensen

Costa

Faou

et al. 2016

Sci Rep

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“…Despite the abundance of SDR enzymes, only a handful of SDR family members have had their affinities for their respective cofactors characterized using ITC. Interestingly, the observed K d for BdcA with NADPH complex is ∼7–15 times higher than that of other members in the immediate SDR family (SDRvv:NADPH, K d = 3.5 µM; ZmRDH:NAD, K d = 2.72 µM; DHDPR:NADPH, K d = 1.5 µM) [35]–[37]. However, the binding affinity is comparable with other oxidoreductases that are more distantly related (PaGDH:NADH, K d = 18.5 µM; OcDH:NADH: K d = 14 µM) [38], [39].…”

Section: Resultsmentioning

confidence: 97%

BdcA, a Protein Important for Escherichia coli Biofilm Dispersal, Is a Short-Chain Dehydrogenase/Reductase that Binds Specifically to NADPH

et al. 2014

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The Escherichia coli protein BdcA (previously referred to as YjgI) plays a key role in the dispersal of cells from bacterial biofilms, and its constitutive activation provides an attractive therapeutic target for dismantling these communities. In order to investigate the function of BdcA at a molecular level, we integrated structural and functional studies. Our 2.05 Å structure of BdcA shows that it is a member of the NAD(P)(H)-dependent short-chain dehydrogenase/reductase (SDR) superfamily. Structural comparisons with other members of the SDR family suggested that BdcA binds NADP(H). This was demonstrated experimentally using thermal denaturation studies, which showed that BcdA binds specifically to NADPH. Subsequent ITC experiments further confirmed this result and reported a Kd of 25.9 µM. Thus, BdcA represents the newest member of the limited number of oxidoreductases shown to be involved in quorum sensing and biofilm dispersal.

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“…Since then, the enzyme has been characterised from several species including B. cereus (Kimura & Goto, 1977), Bacillus megaterium (Kimura & Goto, 1977), Bacillus subtilis (Kimura, 1975), C. glutamicum (Cremer et al, 1988), Methylophilus methylotrophus (Gunji et al, 2004), M. tuberculosis (Cirilli et al, 2003), S. aureus (Dommaraju et al, 2011;Girish et al, 2011), and T. maritima . DHDPR catalyses the second step in the lysine biosynthesis pathway (Fig.…”

Section: Function Of Dhdprmentioning

confidence: 99%

“…In light of this observation, there has been significant interest in studying the molecular basis of nucleotide preference. All NAD-dependent dehydrogenases contain the consensus sequence GXGXXG or GXXGXXG and conserved acidic amino acids 20-30 residues downstream of this glycine rich region (Dommaraju et al, 2011). The main chain nitrogen of the second residue (X) in the consensus sequence interacts with this conserved acidic residue.…”

Section: Nucleotide Preference Of Bacterial Dhdprmentioning

confidence: 99%