The Three-dimensional Structure of a Mycobacterial DapD Provides Insights into DapD Diversity and Reveals Unexpected Particulars about the Enzymatic Mechanism

Schuldt, Linda; Weyand, Simone; Kefala, Georgia; Weiss, M.S.

doi:10.1016/j.jmb.2009.04.046

Cited by 21 publications

(28 citation statements)

References 52 publications

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“…Crystallographic investigations of the binary complex of Mt DapD with succinyl-CoA [26] and of ternary complexes of DapD [28], [29] are consistent with a nucleophilic attack of the substrate amino group on the carbonyl group of succinyl-CoA. Comparisons of the structures of apo-DapD with that of ligand bound DapD revealed conformational changes upon binding of the substrates that involve several regions of the polypeptide chain [25], [28], [29].…”

Section: Introductionmentioning

confidence: 71%

“…The crystal structures of DapD from Escherichia coli [25], Mycobacterium tuberculosis [26] and Mycobacterium bovis [27] have been published, although the origin of the gene for the latter has been questioned [26]. In addition, the coordinates for DapD from Campylobacter jejuni (2RIJ), Enterococcus feacalis (3CJ8), Brucella melitensis (3EG4), and Yersinia pestis (3GOS) have been deposited in the Protein Data Bank by several Structural Genomics projects.…”

Section: Introductionmentioning

confidence: 99%

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Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion

et al. 2012

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The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 Å resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1ΔdapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.

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Section: Introductionmentioning

confidence: 71%

Section: Introductionmentioning

confidence: 99%

Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion

et al. 2012

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“…The dapD gene encoding THPC-NST is found in a large number of bacterial species including E. coli and Mycobacterium species (Beaman et al, 1997;Richaud et al, 1984;Schuldt et al, 2009). Expression of this gene in E. coli is weakly inhibited by lysine (Ou et al, 2008;Richaud et al, 1984).…”

Section: Tetrahydrodipicolinate N-succinyltransferasementioning

confidence: 99%

“…Expression of this gene in E. coli is weakly inhibited by lysine (Ou et al, 2008;Richaud et al, 1984). THPC-NST enzymes characterised to date are comprised of approximately 290 residues and show greater than 18% sequence identity (Beaman et al, 1997;Richaud et al, 1984;Schuldt et al, 2009). …”

Section: Tetrahydrodipicolinate N-succinyltransferasementioning

confidence: 99%

“…All three domains contribute to inter-subunit contacts. The structure of THPC-NST from other bacterial species have since been determined and show a high degree of similarity to that of M. bovis THPC-NST (Nguyen et al, 2008;Schuldt et al, 2009). Crystal structures of M. bovis THPC-NST in complex with substrate analogs and several forms of coenzyme A have resulted in a model describing substrate binding and catalysis (Beaman et al, 1998(Beaman et al, , 2002.…”

Section: Tetrahydrodipicolinate N-succinyltransferasementioning

confidence: 99%

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Enzymology of Bacterial Lysine Biosynthesis

Dogovski¹,

Atkinson²,

Dommaraju³

et al. 2012

Biochemistry

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Characterization of left‐handed beta helix‐domains, and identification and functional annotation of proteins containing such domains

Prabha

Balaji

2020

Proteins

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Only about 0.3% of the entries in UniProt database have manually curated annotation. Annotation at the molecular level often relies on low‐throughput one‐protein‐at‐a‐time approach. Computational methods bridge this gap by assigning function based on sequence and/or fold similarity. Left‐handed beta helix (LbH) consists of three repeating six‐stranded beta‐strands forming an 18‐mer turn of the helix. Analysis of LbH‐domains showed that variations are found in the number of residues in a beta‐strand (5‐7, 6 being the most common), number of turns (4–10) of the helix, insertions of one or more loops of variable length (0‐36 residues), and the location of loop insertion. An 18‐mer HMM profile was created which identifies LbH‐domain containing proteins using sequence as the only input; the number of false positives is zero when proteins tested were those with known 3D structures. 136 474 entries of TrEMBL database were found to contain LbH‐domain. Rules developed by analyzing LbH‐domain containing acyltransferases, gamma‐class carbonic anhydrases, and nucleotidyltransferases have led to the annotation of 17 389 TrEMBL entries which currently have no functional tag.

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The Three-dimensional Structure of a Mycobacterial DapD Provides Insights into DapD Diversity and Reveals Unexpected Particulars about the Enzymatic Mechanism

Cited by 21 publications

References 52 publications

Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion

Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion

Enzymology of Bacterial Lysine Biosynthesis

Characterization of left‐handed beta helix‐domains, and identification and functional annotation of proteins containing such domains

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