Analysis of <i>Streptomyces coelicolor</i> Phosphopantetheinyl Transferase, AcpS, Reveals the Basis for Relaxed Substrate Specificity

Dall'Aglio, P.; Arthur, Christopher J.; Williams, Christopher; Vasilakis, Konstantinos; Maple, Hannah J.; Crosby, John; Crump, Matthew P.; Hadfield, Andrea T.

doi:10.1021/bi2003668

Cited by 20 publications

(25 citation statements)

References 45 publications

(106 reference statements)

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“…Arginine clusters are involved in binding of phosphate-containing molecules such as nucleotides, NADP, FMN, FAD and acetyl-CoA. 46–48 Moreover, arginine clusters play a crucial role in stabilizing the propionic acid side chains of heme groups and bind frequently to organic acids and negatively charged bioactive compunds. 49,50 Finally, we found a number of arginine clusters stabilized by chlorides, sulfates, phosphates, acids and other molecules commonly present in the buffers used for protein purification and crystallization.…”

Section: Resultsmentioning

confidence: 99%

Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks

2012

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Protein-protein interfaces are often stabilized by a small number of dominant contacts, exemplified by the overrepresentation of arginine residues at oligomerization interfaces. Positively charged arginines are most commonly involved in ion pairs of opposite charge; however, previous work of Scheraga and coworkers described the stable, close range interaction between guanidinium pairs in a solvated environment. To extend this work, we searched over 70 thousand protein structures and complexes for unusual formations of arginine residues supported by the electron density. Symmetry transformations were used to generate full assemblies. Clusters of four to eight arginine residues with Cζ-Cζ distances < 5 Å, organized as rings with 4 to 8 members, stacks of two arginines, and strings of stacked arginines, are commonly located at the interfaces of oligomeric proteins. The positive charge is properly balanced by negatively charged counter ions in about 90% of the cases. We also observed planar stacking of guanidinium groups, bridged by hydrogen bonds and interactions with water molecules. The guanidinium groups are commonly involved in 5 hydrogen bonds with water molecules and acceptor groups from surrounding amino acids. Water molecules have a bridging effect on the arginine pairs, but in some cases small molecular weight chemicals in the crystallization buffer may be misinterpreted as water molecules. In summary, despite electrostatic repulsion, arginines do form various clusters that are exposed to interact with and potentially be controlled or switched by charged metabolites, membrane lipids, nucleic acids or side chains of other proteins. Control of the stability of arginine clusters may play an important role in protein-protein oligomerization, molecular recognition and ligand binding.

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Section: Resultsmentioning

confidence: 99%

Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks

2012

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“…The source of 4′PP for the transferase is CoA, but the enzyme can also use different acylated derivatives of CoA (Fig. 1b) (Dall’Aglio et al 2011). Indeed, it is often the case, since most of the CoA molecules in the cell are in the acylated form (Vallari et al 1987).…”

Section: Functions Of Teiismentioning

confidence: 99%

Roles of type II thioesterases and their application for secondary metabolite yield improvement

Kotowska

Pawlik

2014

Appl Microbiol Biotechnol

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A large number of antibiotics and other industrially important microbial secondary metabolites are synthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). These multienzymatic complexes provide an enormous flexibility in formation of diverse chemical structures from simple substrates, such as carboxylic acids and amino acids. Modular PKSs and NRPSs, often referred to as megasynthases, have brought about a special interest due to the colinearity between enzymatic domains in the proteins working as an “assembly line” and the chain elongation and modification steps. Extensive efforts toward modified compound biosynthesis by changing organization of PKS and NRPS domains in a combinatorial manner laid good grounds for rational design of new structures and their controllable biosynthesis as proposed by the synthetic biology approach. Despite undeniable progress made in this field, the yield of such “unnatural” natural products is often not satisfactory. Here, we focus on type II thioesterases (TEIIs)—discrete hydrolytic enzymes often encoded within PKS and NRPS gene clusters which can be used to enhance product yield. We review diverse roles of TEIIs (removal of aberrant residues blocking the megasynthase, participation in substrate selection, intermediate, and product release) and discuss their application in new biosynthetic systems utilizing PKS and NRPS parts.

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“…The crystal structure of Sfp and the studied protein complex with PCP revealed that Sfp has a pseudo-homodimeric fold and provides one V-shaped interface for the 4′-PP cofactor modification of a PCP (Figure 2c); in comparison AcpS is crystallized as a symmetric homo-trimer and three catalytic sites for the post-translational modification of ACPs are located in the interface of AcpS monomers (Figure 2d). 145-147 ACPs and PCPs had been shown to comprise of a three to four helix bundle, whereas the third helix is described as a short α- or 3 10 - helix. However, X-ray studies did not deal with the structural flexibility and dynamics, essential for the function of carrier proteins to shuttle to, interact with, and present their tethered, growing acyl chain to every catalytic domain in any NRPS/PKS/FAS module.…”

Section: A Peptidyl Carrier Protein-centered View Of Nrps Assemblymentioning

confidence: 99%

Structural insights into nonribosomal peptide enzymatic assembly lines

2009

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Nonribosomal peptides have a variety of medicinal activities including activity as antibiotics, antitumor drugs, immunosuppressives, and toxins. Their biosynthesis on multimodular assembly lines as a series of covalently tethered thioesters, in turn covalently attached on pantetheinyl arms on carrier protein way stations, reflects similar chemical logic and protein machinery to fatty acid and polyketide biosynthesis. While structural information on excised or isolated catalytic adenylation (A), condensation (C), peptidyl carrier protein (PCP) and thioesterase (TE) domains had been gathered over the past decade, little was known about how the NRPS catalytic and carrier domains interact with each other both within and across elongation or termination modules. This highlight reviews recent breakthrough achievements in both X-ray and NMR spectroscopic studies that illuminate the architecture of NRPS PCP domains, PCP-containing didomain-fragments and of a full termination module (C-A-PCP-TE).

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Analysis of Streptomyces coelicolor Phosphopantetheinyl Transferase, AcpS, Reveals the Basis for Relaxed Substrate Specificity

Cited by 20 publications

References 45 publications

Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks

Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks

Roles of type II thioesterases and their application for secondary metabolite yield improvement

Structural insights into nonribosomal peptide enzymatic assembly lines

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