Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis |
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Authors: | Qing Yao Jixin Cui Jiayi Wang Ting Li Xiaobo Wan Tianming Luo Yi-Nan Gong Ying Xu Niu Huang Feng Shao |
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Affiliation: | aCollege of Biological Sciences, China Agricultural University, Beijing 100094, China;;bNational Institute of Biological Sciences, Beijing 102206, China; and;cGraduate School of Chinese Academy of Medical Sciences and Beijing Union Medical College, Beijing 100730, China |
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Abstract: | Targeting eukaryotic proteins for deamidation modification is increasingly appreciated as a general bacterial virulence mechanism. Here, we present an atomic view of how a bacterial deamidase effector, cycle-inhibiting factor homolog in Burkholderia pseudomallei (CHBP), recognizes its host targets, ubiquitin (Ub) and Ub-like neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), and catalyzes site-specific deamidation. Crystal structures of CHBP–Ub/NEDD8 complexes show that Ub and NEDD8 are similarly cradled by a large cleft in CHBP with four contacting surfaces. The pattern of Ub/NEDD8 recognition by CHBP resembles that by the E1 activation enzyme, which critically involves the Lys-11 surface in Ub/NEDD8. Close examination of the papain-like catalytic center reveals structural determinants of CHBP being an obligate glutamine deamidase. Molecular-dynamics simulation identifies Gln-31/Glu-31 of Ub/NEDD8 as one key determinant of CHBP substrate preference for NEDD8. Inspired by the idea of using the unique bacterial activity as a tool, we further discover that CHBP-catalyzed NEDD8 deamidation triggers macrophage-specific apoptosis, which predicts a previously unknown macrophage-specific proapoptotic signal that is negatively regulated by neddylation-mediated protein ubiquitination/degradation. |
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Keywords: | Cullin neddylation type III secretion system enteropathogenic E. coli transglutamination MLN4924 |
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