Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-producing enzyme

2019 ◽  
Vol 205 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Tomohiko Matsuzawa ◽  
Masahiro Watanabe ◽  
Yusuke Nakamichi ◽  
Zui Fujimoto ◽  
Katsuro Yaoi
Keyword(s):  
Crystal Structure ◽  
Aspergillus Oryzae ◽  
Substrate Recognition ◽  
Recognition Mechanism

scholarly journals Structural basis for the substrate recognition of aminoglycoside 7′′-phosphotransferase-Ia from Streptomyces hygroscopicus

2019 ◽  
Vol 75 (9) ◽  
pp. 599-607
Author(s):  
Mihoko Takenoya ◽  
Tatsuro Shimamura ◽  
Ryuji Yamanaka ◽  
Yuya Adachi ◽  
Shinsaku Ito ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Recognition ◽  
Streptomyces Hygroscopicus ◽  
Structural Basis ◽  
Hydroxyl Groups ◽  
Recognition Mechanism ◽  
Conserved Residues ◽  
Helical Domain ◽  
Structural Differences ◽  
Aminoglycoside Phosphotransferases

Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7′′-phosphotransferase-Ia [APH(7′′)-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7′′ and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7′′)-Ia and APH(4)-Ia, the crystal structure of APH(7′′)-Ia complexed with HygB is reported. The overall structure of APH(7′′)-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7′′)-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7′′)-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.

scholarly journals Crystal Structure of Chitosanase fromBacillus circulansMH-K1 at 1.6-Å Resolution and Its Substrate Recognition Mechanism

1999 ◽  
Vol 274 (43) ◽  
pp. 30818-30825 ◽  
Author(s):  
Jun-ichi Saito ◽  
Akiko Kita ◽  
Yoshiki Higuchi ◽  
Yoshiho Nagata ◽  
Akikazu Ando ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Recognition ◽  
Recognition Mechanism

scholarly journals Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition.

1994 ◽  
Vol 269 (34) ◽  
pp. 21526-21531 ◽  
Author(s):  
J.C. Fontecilla-Camps ◽  
R. de Llorens ◽  
M.H. le Du ◽  
C.M. Cuchillo
Keyword(s):  
Crystal Structure ◽  
Direct Evidence ◽  
Substrate Recognition

scholarly journals Novel Inhibitor for Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis and Details of Substrate-recognition Mechanism

2008 ◽  
Vol 375 (3) ◽  
pp. 708-719 ◽  
Author(s):  
Yue Xu ◽  
Yoshitaka Nakajima ◽  
Kiyoshi Ito ◽  
Heng Zheng ◽  
Hiroshi Oyama ◽  
...  
Keyword(s):  
Porphyromonas Gingivalis ◽  
Substrate Recognition ◽  
Recognition Mechanism

scholarly journals Arterivirus nsp4 Antagonizes Interferon Beta Production by Proteolytically Cleaving NEMO at Multiple Sites

2019 ◽  
Vol 93 (12) ◽  
Author(s):  
Jiyao Chen ◽  
Dang Wang ◽  
Zheng Sun ◽  
Li Gao ◽  
Xinyu Zhu ◽  
...  
Keyword(s):  
Immune Evasion ◽  
Interferon Beta ◽  
Substrate Recognition ◽  
Innate Immune ◽  
Equine Arteritis Virus ◽  
Single Site ◽  
Respiratory Syndrome Virus ◽  
Type I ◽  
Type I Ifn ◽  
Recognition Mechanism

ABSTRACTEquine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV) represent two members of the familyArteriviridaeand pose major threats for the horse- and swine-breeding industries worldwide. A previous study suggested that PRRSV nsp4, a 3C-like protease, antagonizes interferon beta (IFN-β) production by cleaving the NF-κB essential modulator (NEMO) at a single site, glutamate 349 (E349). Here, we demonstrated that EAV nsp4 also inhibited virus-induced IFN-β production by targeting NEMO for proteolytic cleavage and that the scission occurred at four sites: E166, E171, glutamine 205 (Q205), and E349. Additionally, we found that, besides the previously reported cleavage site E349 in NEMO, scission by PRRSV nsp4 took place at two additional sites, E166 and E171. These results imply that while cleaving NEMO is a common strategy utilized by EAV and PRRSV nsp4 to antagonize IFN induction, EAV nsp4 adopts a more complex substrate recognition mechanism to target NEMO. By analyzing the abilities of the eight different NEMO fragments resulting from EAV or PRRSV nsp4 scission to induce IFN-β production, we serendipitously found that a NEMO fragment (residues 1 to 349) could activate IFN-β transcription more robustly than full-length NEMO, whereas all other NEMO cleavage products were abrogated for the IFN-β-inducing capacity. Thus, NEMO cleavage at E349 alone may not be sufficient to completely inactivate the IFN response via this signaling adaptor. Altogether, our findings suggest that EAV and PRRSV nsp4 cleave NEMO at multiple sites and that this strategy is critical for disarming the innate immune response for viral survival.IMPORTANCEThe arterivirus nsp4-encoded 3C-like protease (3CLpro) plays an important role in virus replication and immune evasion, making it an attractive target for antiviral therapeutics. Previous work suggested that PRRSV nsp4 suppresses type I IFN production by cleaving NEMO at a single site. In contrast, the present study demonstrates that both EAV and PRRSV nsp4 cleave NEMO at multiple sites and that this strategy is essential for disruption of type I IFN production. Moreover, we reveal that EAV nsp4 also cleaves NEMO at glutamine 205 (Q205), which is not targeted by PRRSV nsp4. Notably, targeting a glutamine in NEMO for cleavage has been observed only with picornavirus 3C proteases (3Cpro) and coronavirus 3CLpro. In aggregate, our work expands knowledge of the innate immune evasion mechanisms associated with NEMO cleavage by arterivirus nsp4 and describes a novel substrate recognition characteristic of EAV nsp4.

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