An Affinity Prediction Approach for the Ligand of E3 Ligase Cbl-b and An Insight into Substrate Binding Pattern

2021 ◽  
pp. 116130
Author(s):  
Lv-Bin Hu ◽  
Xiu-Qi Hu ◽  
Qiong Zhang ◽  
Qi-Dong You ◽  
Zheng-Yu Jiang
2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Ying-Yi Huo ◽  
Suhua Li ◽  
Jing Huang ◽  
Zhen Rong ◽  
Zhao Wang ◽  
...  

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>


Structure ◽  
2001 ◽  
Vol 9 (5) ◽  
pp. 419-429 ◽  
Author(s):  
Constanze Breithaupt ◽  
Jochen Strassner ◽  
Ulrike Breitinger ◽  
Robert Huber ◽  
Peter Macheroux ◽  
...  

2011 ◽  
Vol 412 (3) ◽  
pp. 466-480 ◽  
Author(s):  
Folmer Fredslund ◽  
Maher Abou Hachem ◽  
René Jonsgaard Larsen ◽  
Pernille Gerd Sørensen ◽  
Pedro M. Coutinho ◽  
...  

2014 ◽  
Vol 197 (3) ◽  
pp. 510-517 ◽  
Author(s):  
Fan Zhu ◽  
Hua Zhang ◽  
Hui Wu

Serine-rich repeat glycoproteins (SRRPs) are highly conserved in streptococci and staphylococci. Glycosylation of SRRPs is important for bacterial adhesion and pathogenesis.Streptococcus agalactiaeis the leading cause of bacterial sepsis and meningitis among newborns. Srr2, an SRRP fromS. agalactiaestrain COH1, has been implicated in bacterial virulence. Four genes (gtfA,gtfB,gtfC, and gtfD) located downstream ofsrr2share significant homology with genes involved in glycosylation of other SRRPs. We have shown previously thatgtfAandgtfBencode two glycosyltransferases, GtfA and GtfB, that catalyze the transfer of GlcNAc residues to the Srr2 polypeptide. However, the function of other glycosyltransferases in glycosylation of Srr2 is unknown. In this study, we determined that GtfC catalyzed the direct transfer of glucosyl residues to Srr2-GlcNAc. The GtfC crystal structure was solved at 2.7 Å by molecular replacement. Structural analysis revealed a loop region at the N terminus as a putative acceptor substrate binding domain. Deletion of this domain rendered GtfC unable to bind to its substrate Srr2-GlcNAc, concurrently abolished the glycosyltransferase activity of GtfC, and also altered glycosylation of Srr2. Furthermore, deletion of the corresponding regions from GtfC homologs also abolished their substrate binding and enzymatic activity, indicating that this region is functionally conserved. In summary, we have determined that GtfC is important for the glycosylation of Srr2 and identified a conserved loop region that is crucial for acceptor substrate binding from GtfC homologs in streptococci. These findings shed new mechanistic insight into this family of glycosyltransferases.


MedChemComm ◽  
2017 ◽  
Vol 8 (5) ◽  
pp. 1121-1130 ◽  
Author(s):  
L. J. Y. M. Swier ◽  
L. Monjas ◽  
F. Reeßing ◽  
R. C. Oudshoorn ◽  
Aisyah Aisyah ◽  
...  

Exploring binding opportunities in the pocket of ThiT, a S-component for the transport of thiamine.


2008 ◽  
Vol 283 (32) ◽  
pp. 22316-22324 ◽  
Author(s):  
Pravas Kumar Baral ◽  
Nina Jajčanin-Jozić ◽  
Sigrid Deller ◽  
Peter Macheroux ◽  
Marija Abramić ◽  
...  

Biochemistry ◽  
2009 ◽  
Vol 48 (15) ◽  
pp. 3370-3377 ◽  
Author(s):  
Ingrid Dreveny ◽  
Aleksandra S. Andryushkova ◽  
Anton Glieder ◽  
Karl Gruber ◽  
Christoph Kratky

2018 ◽  
Author(s):  
Magdalena J. Mazur ◽  
Mark Kwaaitaal ◽  
Manuel Arroyo Mateos ◽  
Francesca Maio ◽  
Ramachandra K. Kini ◽  
...  

One sentence SummarySUMO conjugation activity causes formation of SUMO nuclear bodies, which strongly overlap with COP1 bodies thanks to a substrate-binding (VP) motif in the E3 ligase SIZ1 that acts as bridge protein.AbstractAttachment of the small ubiquitin-like modifier SUMO to substrate proteins modulates their turnover, activity or interaction partners. An unresolved question is how this SUMO conjugation activity concentrates the enzymes involved and the substrates into uncharacterized nuclear bodies (NBs). We here define the requirements for the formation of SUMO NBs and for their subsequent co-localisation with the master regulator of growth, the E3 ubiquitin ligase COP1. COP1 activity results in degradation of transcription factors, which primes the transcriptional response that underlies elongation growth induced by night-time and high ambient temperatures (skoto- and thermomorphogenesis, respectively). SUMO conjugation activity itself is sufficient to target the SUMO machinery into NBs. Co-localization of these bodies with COP1 requires besides SUMO conjugation activity, a SUMO acceptor site in COP1 and the SUMO E3 ligase SIZ1. We find that SIZ1 docks in the substrate-binding pocket of COP1 via two VP motifs - a known peptide motif of COP1 substrates. The data reveal that SIZ1 physically connects COP1 and SUMO conjugation activity in the same NBs that can also contain the blue-light receptors CRY1 and CRY2. Our findings thus suggest that sumoylation apparently coordinates COP1 activity inside these NBs; a mechanism that potentially explains how SIZ1 and SUMO both control the timing and amplitude of the high-temperature growth response. The strong co-localization of COP1 and SUMO in these NBs might also explain why many COP1 substrates are sumoylated.Funding informationThe Netherlands Scientific Organisation (ALW-VIDI grant 864.10.004 to HvdB) and the Topsector T&U program Better Plants for Demands (grant 1409-036 to HvdB), including the partnering breeding companies, supported this work; FM is financially supported by Keygene N.V. (The Netherlands).


2020 ◽  
Author(s):  
Jianxiao Wu ◽  
Simon B. Eickhoff ◽  
Felix Hoffstaedter ◽  
Kaustubh R. Patil ◽  
Holger Schwender ◽  
...  

AbstractThe recent availability of population-based studies with neuroimaging and behavioral measurements opens promising perspectives to investigate the relationships between interindividual variability in brain regions’ connectivity and behavioral phenotypes. However, the multivariate nature of connectivity-based prediction model severely limits the insight into brain-behavior patterns for neuroscience. To address this issue, we propose a connectivity-based psychometric prediction framework based on individual regions’ connectivity profiles. We first illustrate two main applications: 1) single brain region’s predictive power for a range of psychometric variables 2) single psychometric variable’s predictive power variation across brain region. We compare the patterns of brain-behavior provided by these approaches to the brain-behavior relationships from activation approaches. Then, capitalizing on the increased transparency of our approach, we demonstrate how the influence of various data processing and analyses can directly influence the patterns of brain-behavior relationships. Such region-based prediction approach can hence contribute to neurobiological validity in the study of brain-behavior relationships.


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