Structural Insight into Binding of the ZZ Domain of HERC2 to Histone H3 and SUMO1

Liu, Jiuyang; Xue, Zhaoyu; Zhang, Yi; Vann, Kendra R.; Shi, Xiaobing; Kutateladze, Tatiana G.

doi:10.1016/j.str.2020.07.003

Cited by 9 publications

(22 citation statements)

References 22 publications

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“…Ams1 forms a tetramer in the complex structure (Figure 4A and 4B), as in the free Ams1 structure (Zhang et al, 2020). Nbr1-ZZ1 adopts a cross-brace zinc finger fold that coordinates two zinc ions and contains an N-terminal hairpin loop (a two-stranded β-sheet in some ZZ domains), a three-stranded antiparallel β-sheet, and an α-helix (Figure 4C), similar to other ZZ domain structures (Ponting et al, 1996; Cha-Molstad et al, 2017; Kwon et al, 2018; Zhang et al, 2018a; Mi et al, 2018; Zhang et al, 2018b; Liu et al, 2020). Four Nbr1-ZZ1 molecules bind symmetrically to one Ams1 tetramer (Figure 4A and 4B).…”

Section: Resultsmentioning

confidence: 80%

“…Its homologs in diverse eukaryotic organisms, including human NBR1, also possess one or multiple ZZ domains (Kraft et al, 2010). ZZ domains are approximately 50-amino-acid long domains containing two structural zinc ions (Ponting et al, 1996; Legge et al, 2004; Zhang et al, 2019), and are known to mediate protein-protein interactions (Liu et al, 2015; Cha-Molstad et al, 2017; Kwon et al, 2018; Zhang et al, 2018a; Mi et al, 2018; Zhang et al, 2018b; Liu et al, 2020; Danielsen et al, 2012). Our previous study showed that the second and the third ZZ domains (ZZ2-ZZ3) of Nbr1 together mediate its interactions with NVT cargos Lap2 and Ape2 (Liu et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, several atomic structures of ZZ domains in complex with ligand peptides have been solved by X-ray crystallography or NMR spectroscopy, including the ZZ domain of p62/SQSTM1 bound to N-degron peptides (Kwon et al, 2018; Zhang et al, 2018b), the ZZ domains of p300 and ZZZ3 bound to an N-terminal peptide of histone H3 (Zhang et al, 2018a; Mi et al, 2018), and the ZZ domain of HERC2 bound separately to N-terminal peptides of histone H3 and SUMO (Liu et al, 2020). These structures revealed a common theme of ZZ-mediated binding: ZZ domains bind the N-termini of their interacting proteins.…”

Section: Introductionmentioning

confidence: 99%

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Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1

Wang

Zhang

Liu

et al. 2021

Preprint

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In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.

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Section: Resultsmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1

Wang

Zhang

Liu

et al. 2021

Preprint

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“…The crystal structures of HERC2 ZZ linked to H3 1–6 and SUMO1 1–6 were determined using materials and software listed in the Key Resources Table . Statistics generated from X-ray crystallography data processing, refinement, and structure validation is described in ( Liu et al., 2020 ).…”

Section: Quantification and Statistical Analysismentioning

confidence: 99%

“…This methodology could be applied for characterization of binding activities of other histone readers. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020) .…”

mentioning

confidence: 99%

Protocol for Biochemical Analysis and Structure Determination of the ZZ Domain of the E3 Ubiquitin Ligase HERC2

et al. 2020

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Summary Since its discovery, several ligands of the ZZ domain have been identified; however, molecular and structural information underlying binding of these ligands remains limited. Here, we describe a protocol for biochemical and structural analysis of the ZZ domain of human E3 ubiquitin ligase HERC2 (HERC2 ZZ ) and its interaction with its ligands: the N-terminal tails of histone H3 and SUMO1. This methodology could be applied for characterization of binding activities of other histone readers. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020) .

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Structural and biophysical characterization of the nucleosome-binding PZP domain

et al. 2021

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Summary The core subunit of the MORF acetyltransferase complex BRPF1 contains a unique combination of zinc fingers, including a plant homeodomain (PHD) finger followed by a zinc knuckle and another PHD finger, which together form a PZP domain (BRPF1 PZP ). BRPF1 PZP has been shown to bind to the nucleosome and make contacts with both histone H3 tail and DNA. Here, we describe biophysical and structural methods for characterization of the interactions between BRPF1 PZP , H3 tail, DNA, and the intact nucleosome. For complete details on the use and execution of this protocol, please refer to Klein et al. (2020) .

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Structural Insight into Binding of the ZZ Domain of HERC2 to Histone H3 and SUMO1

Cited by 9 publications

References 22 publications

Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1

Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1

Protocol for Biochemical Analysis and Structure Determination of the ZZ Domain of the E3 Ubiquitin Ligase HERC2

Structural and biophysical characterization of the nucleosome-binding PZP domain

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