Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor

Fujishiro, Takashi; Kahnt, Jörg; Ermler, Ulrich; Shima, Seigo

doi:10.1038/ncomms7895

Cited by 27 publications

(37 citation statements)

References 53 publications

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“…The former involves a 5-member ring a1 and has a distance (angle) of 4.0 Å (7.4 deg), and the latter involves a 6-member ring a2 and has a distance (angle) of 4.0 Å (6.3 deg). ATP bound to Hmd co-occurring protein HcgE from Methanothermobacter marburgensis forms two perpendicular interactions with Y91 (Figure 4D, PDB-ID: 3wv8, chain B) [59] . In this complex structure, Y 6 :5 (ring a1) has a distance of 5.1 Å and an angle of 76.9 deg, whereas Y 6 :6 (ring a2) has a distance of 5.1 Å and an angle of 77.2 deg.…”

Section: Resultsmentioning

confidence: 99%

“…ATP bound to Hmd co-occurring protein HcgE from Methanothermobacter marburgensis forms two perpendicular interactions with Y91 (Figure 4d, PDB-ID: 3wv8, chain B). [58] In this complex structure, Y 6 :5 (ring a1) has a distance of 5.1 Å and an angle of 76.9°, whereas Y 6 :6 (ring a2) has a distance of 5.1 Å and an angle of 77.2°. Figure 5 presents three examples of ligand-protein complexes stabilized by multiple aromatic interactions involving tryptophan and histidine residues.…”

Section: Examples Of Aromatic Interactions Stabilizing Ligand-protementioning

confidence: 95%

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Aromatic interactions at the ligand–protein interface: Implications for the development of docking scoring functions

Bryliński

2017

Chem Biol Drug Des

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The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand-protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π-π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as the benzene dimer. Many contemporary ligand docking programs implicitly treat aromatic stacking with van der Waals and Coulombic potentials. Although this approach generally provides a sufficient specificity to model aromatic interactions, the geometry of π-π contacts in high-scoring docking conformations could still be improved. The comprehensive analysis of aromatic geometries at ligand-protein interfaces lies the foundation for the development of type-specific statistical potentials to more accurately describe aromatic interactions in molecular docking. A Perl script to detect and calculate the geometric parameters of aromatic interactions in ligand-protein complexes is available at https://github.com/michal-brylinski/earomatic. The dataset comprising experimental complex structures and computer-generated models is available at https://osf.io/rztha/.

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Section: Resultsmentioning

confidence: 99%

Section: Examples Of Aromatic Interactions Stabilizing Ligand-protementioning

confidence: 95%

Aromatic interactions at the ligand–protein interface: Implications for the development of docking scoring functions

Bryliński

2017

Chem Biol Drug Des

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“…We have previously successfully predicted the catalytic function of several proteins based on the crystal structure and on subsequent in vitro activity studies for verification (structure-to-function approach) [35,36]. In this study, structural together with infrared spectroscopic and kinetic data clearly excluded most of the postulated functions of HmdII and we present a hypothesis about its cellular role of methylene-H 4 MPT sensor.…”

Section: Discussionmentioning

confidence: 82%

“…The structure of the loop region after the strand 13 : 17 directly involved in the FeGP cofactor binding is largely conserved, but adjacent regions that pack against it as the two-helical segment (residues [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] and the helical region (residues 68-115) of Hmd are truncated in HmdII. Apparently, the FeGP cofactor binding site is more loosely anchored with the rest of the protein in HmdII than in Hmd.…”

Section: X-ray Structure Analysis Of Hmdii Of Methanocaldococcus Jannmentioning

confidence: 99%

Towards a functional identification of catalytically inactive [Fe]‐hydrogenase paralogs

et al. 2015

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[Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H₂ cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H₄MPT⁺). Most hydrogenotrophic methanogens contain the hmd-related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute the HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H₄MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme–methylene-H₄MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H₄MPT⁺ compared with Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turnover process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared with in Hmd, which impairs the catalytically necessary open-to-close transition, and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H₂ sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthetases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H₄MPT concentration

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“…HcgE was identified as an adenylyltransferase that adenylylates the 6-carboxy group of 1.Asubsequent transesterification reaction is catalyzed by HcgF by using an inherent cysteine that forms at hioester bond with 1.T he thioester is proposed to be ad irect precursor of acyl-ironb ond biosynthesis. [6] ForH cgD,afunction as an iron-trafficking protein was proposed. [7] Thefunctions of HcgA, HcgC,and HcgG are unknown.…”

mentioning

confidence: 99%

Identification of HcgC as a SAM‐Dependent Pyridinol Methyltransferase in [Fe]‐Hydrogenase Cofactor Biosynthesis

Fujishiro

Bai

et al. 2016

Angew Chem Int Ed

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Previous retrosynthetic and isotope-labeling studies have indicated that biosynthesis of the iron guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase requires a methyltransferase. This hypothetical enzyme covalently attaches the methyl group at the 3-position of the pyridinol ring. We describe the identification of HcgC, a gene product of the hcgA-G cluster responsible for FeGP cofactor biosynthesis. It acts as an S-adenosylmethionine (SAM)-dependent methyltransferase, based on the crystal structures of HcgC and the HcgC/SAM and HcgC/S-adenosylhomocysteine (SAH) complexes. The pyridinol substrate, 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol, was predicted based on properties of the conserved binding pocket and substrate docking simulations. For verification, the assumed substrate was synthesized and used in a kinetic assay. Mass spectrometry and NMR analysis revealed 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol as the reaction product, which confirmed the function of HcgC.

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Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor

Cited by 27 publications

References 53 publications

Aromatic interactions at the ligand–protein interface: Implications for the development of docking scoring functions

Aromatic interactions at the ligand–protein interface: Implications for the development of docking scoring functions

Towards a functional identification of catalytically inactive [Fe]‐hydrogenase paralogs

Identification of HcgC as a SAM‐Dependent Pyridinol Methyltransferase in [Fe]‐Hydrogenase Cofactor Biosynthesis

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