title: Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis.
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.
authors.affiliation: College of Biological Sciences, China Agricultural University, Beijing 100094,  China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Yao
authors.forename: Jixin
authors.initials: J
authors.lastname: Cui
authors.forename: Jiayi
authors.initials: J
authors.lastname: Wang
authors.forename: Ting
authors.initials: T
authors.lastname: Li
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Wan
authors.forename: Tianming
authors.initials: T
authors.lastname: Luo
authors.forename: Yi-Nan
authors.initials: YN
authors.lastname: Gong
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
authors.forename: Niu
authors.initials: N
authors.lastname: Huang
authors.forename: Feng
authors.initials: F
authors.lastname: Shao
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017209:Apoptosis / Q000502:physiology*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D016957:Burkholderia pseudomallei / Q000235:genetics / Q000378:metabolism / Q000472:pathogenicity; D002460:Cell Line; D018360:Crystallography, X-Ray; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D008264:Macrophages / Q000166:cytology* / Q000502:physiology*; D051379:Mice; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D046912:Multiprotein Complexes / Q000737:chemistry / Q000378:metabolism; D016297:Mutagenesis, Site-Directed; D000075687:NEDD8 Protein; D017386:Sequence Homology, Amino Acid; D055672:Static Electricity; D014452:Ubiquitins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D046912:Multiprotein Complexes; D000075687:NEDD8 Protein; C082860:NEDD8 protein, human; D014452:Ubiquitins