Structures of Glycinamide Ribonucleotide Transformylase (PurN) from Mycobacterium tuberculosis Reveal a Novel Dimer with Relevance to Drug Discovery

Zhang, Zhening; Caradoc-Davies, Tom T.; Dickson, James M.; Baker, Edward N.; Squire, C.J.

doi:10.1016/j.jmb.2009.04.044

Cited by 15 publications

(18 citation statements)

References 32 publications

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“…ProMOL still finds 15 of 31 3 homologs of PDB entry 1CDE [23], a serine-containing member of EC class 2.1.2.2. A motif based on the active site of PDB entry 3DA8 [24], which contains a threonine in place of the serine in the active site, aligned with 12 of 31 3 homologs. This includes 7 that aligned with 1CDE (with a Levenshtein distance of 1, reflecting the threonine for serine substitution) and 5 that were uniquely aligned to 3DA8.…”

Section: Resultsmentioning

confidence: 99%

Automated protein motif generation in the structure-based protein function prediction tool ProMOL

Osipovitch

Lambrecht

Baker

et al. 2015

J Struct Funct Genomics

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ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077.

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Section: Resultsmentioning

confidence: 99%

Automated protein motif generation in the structure-based protein function prediction tool ProMOL

Osipovitch

Lambrecht

Baker

et al. 2015

J Struct Funct Genomics

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“…The function of most normal cells (except liver and T cells) relies on the salvage of purines, whereas tumour cells cannot salvage purines efficiently and depend on de novo synthesis (McGuire, 2003;Zhang et al, 2009). The de novo purine-biosynthesis pathway consists of ten enzymatic reactions (Gooljarsingh et al, 2001;Hartman & Buchanan, 1959;Welin et al, 2010), two of which involve folate-dependent enzymes: phosphoribosylglycinamide formyltransferase (PurN) and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase (PurH).…”

Section: Introductionmentioning

confidence: 99%

“…The de novo purine-biosynthesis pathway consists of ten enzymatic reactions (Gooljarsingh et al, 2001;Hartman & Buchanan, 1959;Welin et al, 2010), two of which involve folate-dependent enzymes: phosphoribosylglycinamide formyltransferase (PurN) and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase (PurH). PurN catalyses the third step of the purine-biosynthesis pathway and transfers the formyl group from N 10 -formyltetrahydrofolate (fTHF) to glycinamide ribonucleotide (GAR) to produce formyl-glycinamide ribonucleotide (fGAR) and tetrahydrofolate (Almassy et al, 1992;Zhang et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…Structures are available of three bacterial PurN enzymes, those from Escherichia coli (PDB entries 1cde and 1grc; Almassy et al, 1992;Chen et al, 1992), Aquifex aeolicus (PDB code 2ywr; W. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai & G. Sampei, unpublished work) and Mycobacterium tuberculosis (PDB entries 3dcj and 3da8; Zhang et al, 2009), and one eukaryotic enzyme, the PurN domain of a trifunctional three-domain human enzyme (PDB entry 1zlx; Zhang et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

“…The reported crystal structures of E. coli and human PurN contain numerous examples of ligand binding, including the substrate GAR, cofactor analogues and cofactor-based inhibitors, as well as structures with multisubstrate adduct inhibitors (Zhang et al, 2002(Zhang et al, , 2009Almassy et al, 1992). This wealth of information has played a major part in the structure-based drug discovery of antifolate compounds for cancer chemotherapy and provides an important knowledge base for the design of potential antibacterial agents once the similarities and differences between the bacterial and human enzymes have been mapped.…”

Section: Introductionmentioning

confidence: 99%

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Expression, crystallization and preliminary X-ray analysis of the phosphoribosylglycinamide formyltransferase fromStreptococcus mutans

et al. 2011

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Phosphoribosylglycinamide formyltransferase (PurN) from Streptococcus mutans was recombinantly expressed in Escherichia coli. An effective purification protocol was established. The purified protein, which had a purity of >95%, was identified by SDS-PAGE and MALDI-TOF MS. The protein was crystallized using the vapour-diffusion method in hanging-drop mode with PEG 3350 as the primary precipitant. X-ray diffraction data were collected to 2.1 Å resolution. Preliminary X-ray analysis indicated that the crystal belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 52.25, b = 63.29, c = 131.81 Å .

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PvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase

Kenjić

Hoag

Moraski

et al. 2019

Archives of Biochemistry and Biophysics

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The hydroxyornithine transformylase from Pseudomonas aeruginosa is known by the gene name pvdF, and has been hypothesized to use N 10 -formyltetrahydrofolate (N 10 -fTHF) as a co-substrate formyl donor to convert N 5 -hydroxyornithine (OHOrn) to N 5 -formyl-N 5 -hydroxyornithine (fOHOrn). PvdF is in the biosynthetic pathway for pyoverdin biosynthesis, a siderophore generated under iron-limiting conditions that has been linked to virulence, quorum sensing and biofilm formation. The structure of PvdF was determined by X-ray crystallography to 2.3 Å, revealing a formyltransferase fold consistent with N 10 -formyltetrahydrofolate dependent enzymes, such as the glycinamide ribonucleotide transformylases, N-sugar transformylases and methionyl-tRNA transformylases. Whereas the core structure, including the catalytic triad, is conserved, PvdF has three insertions of 18 or more amino acids, which we hypothesize are key to binding the OHOrn substrate. Steady state kinetics revealed a non-hyperbolic rate curve, promoting the hypothesis that PvdF uses a random-sequential mechanism, and favors folate binding over OHOrn.

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Structures of Glycinamide Ribonucleotide Transformylase (PurN) from Mycobacterium tuberculosis Reveal a Novel Dimer with Relevance to Drug Discovery

Cited by 15 publications

References 32 publications

Automated protein motif generation in the structure-based protein function prediction tool ProMOL

Automated protein motif generation in the structure-based protein function prediction tool ProMOL

Expression, crystallization and preliminary X-ray analysis of the phosphoribosylglycinamide formyltransferase fromStreptococcus mutans

PvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase

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