<i>Xanthomonas campestris</i> PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle‐like fold that possibly serves as a PQQ carrier

Tsai, Tung-Yi; Yang, Chih‐Yung; Shih, Hui-Ling; Wang, Andrew H.‐J.; Chou, Shan‐Ho

doi:10.1002/prot.22461

Cited by 33 publications

(36 citation statements)

References 34 publications

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“…In the crystal, XcPqqD adopts a saddle-like dimeric conformation with each monomer, containing an ␣-helix bundle and an extended ␤1-␤2 hairpin feature, interlocked with the another monomer by H-bonds and hydrophobic interactions in an elongated ␤3 strand region (20). By contrast, in solution KpPqqD adopts a monomeric globular structure that is quite different from the crystallized dimer or the monomer of XcPqqD.…”

Section: Discussionmentioning

confidence: 92%

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PqqD Is a Novel Peptide Chaperone That Forms a Ternary Complex with the Radical S-Adenosylmethionine Protein PqqE in the Pyrroloquinoline Quinone Biosynthetic Pathway

Latham

Iavarone

Barr

et al. 2015

Journal of Biological Chemistry

123

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Section: Discussionmentioning

confidence: 92%

“…Analysis of the structure indicates that XcPqqD forms a saddle-like dimer under crystallization conditions (Fig. 2) but little functional information could be derived (20). A bioinformatic analysis on PqqD could not identify functionally relevant residues (15), adding to the ambiguity of the role that PqqD plays in PQQ biogenesis.…”

mentioning

confidence: 99%

PqqD Is a Novel Peptide Chaperone That Forms a Ternary Complex with the Radical S-Adenosylmethionine Protein PqqE in the Pyrroloquinoline Quinone Biosynthetic Pathway

Latham

Iavarone

Barr

et al. 2015

Journal of Biological Chemistry

123

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“…This has been observed in at least some of the enzymes involved in the biosynthesis of pyrroloquinoline quinone (45), lantibiotics (46), lasso peptides (44), and cyanobactins (47). In contrast, the follower peptide binding observed in PCY1 does not rely on hydrophobic interactions, but rather on hydrogenbonding interactions.…”

Section: Resultsmentioning

confidence: 97%

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Chekan

Estrada

Covello

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.RiPP | biosynthesis | peptide | plant | orbitide

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“…3A) PqqD was made available nearly a decade ago (40). From this structure, it was postulated that PqqD could serve as a PQQreleasing mechanism, a scaffold for protein complexes, or as a PQQ carrier (4,40).…”

Section: Toward a Structural Basis Of Protein-protein Interactions Wimentioning

confidence: 99%

At the confluence of ribosomally synthesized peptide modification and radical S-adenosylmethionine (SAM) enzymology

Latham

Barr

Klinman

2017

Journal of Biological Chemistry

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Radical S-adenosylmethionine (RS) enzymology has emerged as a major biochemical strategy for the homolytic cleavage of unactivated C-H bonds. At the same time, the post-translational modification of ribosomally synthesized peptides is a rapidly expanding area of investigation. We discuss the functional cross-section of these two disciplines, highlighting the recently uncovered importance of protein-protein interactions, especially between the peptide substrate and its chaperone, which functions either as a stand-alone protein or as an N-terminal fusion to the respective RS enzyme. The need for further work on this class of enzymes is emphasized, given the poorly understood roles performed by multiple, auxiliary iron-sulfur clusters and the paucity of protein X-ray structural data.Modern biochemistry has seen the exponential growth of two exciting areas of research that focus individually on the post-translational modification of ribosomally synthesized and post-translationally modified peptides (RiPPs) 2 (1) and on the structure and mechanism of free radical conversions catalyzed by radical S-adenosylmethionine (RS) enzymes (2, 3). These separate fields have recently converged within a growing family of enzymes that bring about free radical-based, post-translational modifications on ribosomally produced peptide substrates. RS enzymes function by cleavage of a [4Fe-4S] clusterbound S-adenosylmethionine to form methionine and a deoxyadenosyl radical. This radical then initiates the reaction by abstracting a hydrogen atom from the substrate. The [4Fe-4S] cluster that accomplishes this reaction has a characteristic CX 3 CXC motif, with each of the cysteines coordinated to a single iron, leaving an open coordination sphere where SAM binds and is cleaved. A subset of RS enzymes belongs to a family that contains an additional conserved structural motif annotated as a SPASM domain and referred to as RS-SPASM proteins. Although the exact function of the SPASM domain is unknown, it has been shown that it houses generally two additional iron-sulfur clusters that are critical in RS-SPASM chemistry. Using the perspective of the pathway for production of the bacterial cofactor pyrroloquinoline quinone (PQQ), we compare and highlight some of the unique properties among these RS-SPASM-dependent RiPP systems. Bioinformatics analyses suggest that the family members will extend far beyond the examples presented herein.

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Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle‐like fold that possibly serves as a PQQ carrier

Cited by 33 publications

References 34 publications

PqqD Is a Novel Peptide Chaperone That Forms a Ternary Complex with the Radical S-Adenosylmethionine Protein PqqE in the Pyrroloquinoline Quinone Biosynthetic Pathway

PqqD Is a Novel Peptide Chaperone That Forms a Ternary Complex with the Radical S-Adenosylmethionine Protein PqqE in the Pyrroloquinoline Quinone Biosynthetic Pathway

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

At the confluence of ribosomally synthesized peptide modification and radical S-adenosylmethionine (SAM) enzymology

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