Deciphering key features in protein structures with the new ENDscript server

Robert, Xavier; Gouet, Patrice

doi:10.1093/nar/gku316

Cited by 5,709 publications

(3,907 citation statements)

References 22 publications

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“…Sequence alignment analysis and illustration preparation were performed with CLUSTAL W (Larkin et al, 2007) and ESPript 3.0 (http://espript.ibcp. fr/ESPript/ESPript/; Robert & Gouet, 2014), respectively.…”

Section: Methodsmentioning

confidence: 99%

CphA2 is a novel type of cyanophycin synthetase in N2-fixing cyanobacteria

et al. 2016

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Most cyanobacteria use a single type of cyanophycin synthetase, CphA1, to synthesize the nitrogen-rich polymer cyanophycin. The genomes of many N 2 -fixing cyanobacteria contain an additional gene that encodes a second type of cyanophycin synthetase, CphA2. The potential function of this enzyme has been debated due to its reduced size and the lack of one of the two ATP-binding sites that are present in CphA1. Here, we analysed CphA2 from Anabaena variabilis ATCC 29413 and Cyanothece sp. PCC 7425. We found that CphA2 polymerized the dipeptide b-aspartyl-arginine to form cyanophycin. Thus, CphA2 represents a novel type of cyanophycin synthetase. A cphA2 disruption mutant of A. variabilis was generated. Growth of this mutant was impaired under high-light conditions and nitrogen deprivation, suggesting that CphA2 plays an important role in nitrogen metabolism under N 2 -fixing conditions. Electron micrographs revealed that the mutant had fewer cyanophycin granules, but no alteration in the distribution of granules in its cells was observed. Localization of CphA2 by immunogold electron microscopy demonstrated that the enzyme is attached to cyanophycin granules. Expression of CphA1 and CphA2 was examined in Anabaena WT and cphA mutant cells. Whilst the CphA1 level increased upon nitrogen deprivation, the CphA2 level remained nearly constant.

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Section: Methodsmentioning

confidence: 99%

CphA2 is a novel type of cyanophycin synthetase in N2-fixing cyanobacteria

et al. 2016

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“…The highly conserved "right wall" residues are marked by a red star; the partly conserved "floor" residues are marked by a blue star; the non-conserved "ceiling" residues are marked by a gray star. The alignments were constructed with ClustalW (45) and refined with ESPript (46). also contains a short ␣-helix joining the ␤-hairpin and the zinc finger motifs.…”

Section: Zcwpw2 Morc3 and Morc4 Are Histone H3k4me3mentioning

confidence: 99%

Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins

Liu

Tempel

Zhang

et al. 2016

Journal of Biological Chemistry

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Covalent modifications of histone N-terminal tails play a critical role in regulating chromatin structure and controlling gene expression. These modifications are controlled by histone-modifying enzymes and read out by histone-binding proteins. Numerous proteins have been identified as histone modification readers. Here we report the family-wide characterization of histone binding abilities of human CW domain-containing proteins. We demonstrate that the CW domains in ZCWPW2 and MORC3/4 selectively recognize histone H3 trimethylated at Lys-4, similar to ZCWPW1 reported previously, while the MORC1/2 and LSD2 lack histone H3 Lys-4 binding ability. Our crystal structures of the CW domains of ZCWPW2 and MORC3 in complex with the histone H3 trimethylated at Lys-4 peptide reveal the molecular basis of this interaction. In each complex, two tryptophan residues in the CW domain form the "floor" and "right wall," respectively, of the methyllysine recognition cage. Our mutation results based on ZCWPW2 reveal that the right wall tryptophan residue is essential for binding, and the floor tryptophan residue enhances binding affinity. Our structural and mutational analysis highlights the conserved roles of the cage residues of CW domain across the histone methyllysine binders but also suggests why some CW domains lack histone binding ability.Chromatin structure is dynamically regulated by histone post-translational modifications, such as methylation, acetylation, phosphorylation, ubiquitination, and sumoylation (1). These post-translational modifications constitute the "histone code," which is written or erased by histone-modifying enzymes and recognized by histone code "reader" proteins (2-4).Histone methylation, such as lysine methylation at the ⑀-amino group at levels from mono-to trimethylation (me1-me3), has received extensive attention (5). A number of domains bind methylated histone tails. Prominent examples include the chromodomain, Tudor domain, MBT domain, PWWP domain, and PHD domain (4, 6, 7). The CW domain has recently been identified as a new member of the lysine methylation reader family (8 -11).The CW domain is a zinc binding domain, composed of ϳ50 amino acid residues with four conserved cysteine (C) and two conserved tryptophan (W) residues, and its name was derived from these conserved residues. CW domains are found in chromatin-associated proteins in animals and plants and grouped into 12 families based on sequence similarity (12). There are seven CW domain-containing proteins in humans, namely ZCWPW1, ZCWPW2, MORC1, MORC2, MORC3, MORC4, and LSD2 (Fig. 1A). Prior studies have shown that the CW domains of ZCWPW1 (8), MORC3 (10), and MORC4 (9) are readers of H3K4 3 methylated histones with differing preferences for histone H3K4 methylation states (i.e. ZCWPW1 and MORC3 preferentially recognize histone H3K4me3 (8, 10), whereas the CW domain of human MORC4 prefers dimethylated H3K4 (9)). The LSD2 CW domain is required for the demethylation function of LSD2 but does not bind to any H3K4 peptides (13). However, th...

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“…Numbers in orange circles shown below the alignment represent Cys residues ligating the auxiliary clusters (Aux) in anSMEcpe (Aux I: 1, 2, 3, and 7; Aux II: 4, 5, 6, and 8) (17). The figure was produced using ESPRIPT (52).…”

Section: Expression and Purification Of The Qhpc⅐qhpd Complex-mentioning

confidence: 99%

The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds

Nakai

Ito

Kobayashi

et al. 2015

Journal of Biological Chemistry

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Background:The small subunit of quinohemoprotein amine dehydrogenase contains three Cys-to-Asp/Glu thioether bonds. Results:The radical S-adenosyl-L-methionine (SAM) enzyme QhpD catalyzes the single-turnover reaction of thioether bond formation in the protein substrate. Conclusion:The thioether bond formation by QhpD proceeds sequentially in an N-to C-terminal direction of the polypeptide. Significance: Our findings uncover another challenging reaction of radical SAM superfamily of enzymes.

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Deciphering key features in protein structures with the new ENDscript server

Cited by 5,709 publications

References 22 publications

CphA2 is a novel type of cyanophycin synthetase in N2-fixing cyanobacteria

CphA2 is a novel type of cyanophycin synthetase in N2-fixing cyanobacteria

Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins

The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds

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