The N-terminal ubiquitin-binding region of ubiquitin-specific protease 28 modulates its deubiquitination function: NMR structural and mechanistic insights

2015 ◽  
Vol 471 (2) ◽  
pp. 155-165 ◽  
Author(s):  
Yi Wen ◽  
Li Shi ◽  
Yiluan Ding ◽  
Rong Cui ◽  
Wen-tian He ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Molecular Mechanism ◽  
Structure And Function ◽  
Binding Region ◽  
Ubiquitin Binding ◽  
Specific Protease ◽  
Ubiquitin Specific Protease ◽  
And Function

We have characterized the structure and function of the N-terminal UBR of Usp28 in this study. Our findings are helpful for a better understanding of the underlying molecular mechanism in the control of catalytic activity of DUBs.

The role of UBL domains in ubiquitin-specific proteases

2012 ◽  
Vol 40 (3) ◽  
pp. 539-545 ◽  
Author(s):  
Alex C. Faesen ◽  
Mark P.A. Luna-Vargas ◽  
Titia K. Sixma
Keyword(s):  
Catalytic Activity ◽  
Catalytic Domain ◽  
Mechanisms Of Action ◽  
Deubiquitinating Enzymes ◽  
Activated State ◽  
Ubiquitin Binding ◽  
Specific Protease ◽  
Ubiquitin Conjugation ◽  
Ubiquitin Specific Protease

Ubiquitin conjugation and deconjugation provides a powerful signalling system to change the fate of its target enzymes. Ubiquitination levels are organized through a balance between ubiquitinating E1, E2 and E3 enzymes and deubiquitination by DUBs (deubiquitinating enzymes). These enzymes are tightly regulated to control their activity. In the present article, we discuss the different ways in which DUBs of the USP (ubiquitin-specific protease) family are regulated by internal domains with a UBL (ubiquitin-like) fold. The UBL domain in USP14 is important for its localization at the proteasome, which enhances catalysis. In contrast, a UBL domain in USP4 binds to the catalytic domain and competes with ubiquitin binding. In this process, the UBL domain mimics ubiquitin and partially inhibits catalysis. In USP7, there are five consecutive UBL domains, of which the last two affect catalytic activity. Surprisingly, they do not act like ubiquitin and activate catalysis rather than inhibiting it. These C-terminal UBL domains promote a conformational change that allows ubiquitin binding and organizes the catalytic centre. Thus it seems that UBL domains have different functions in different USPs. Other proteins can modulate the roles of UBL domains in USP4 and USP7. On one hand, the inhibition of USP4 can be relieved when the UBL is sequestered by another USP. On the other, the activation of USP7 is increased, when the UBL-activated state is stabilized by allosteric binding of GMP synthetase. Altogether, UBL domains appear to be able to regulate catalytic activity in USPs, but they can use widely different mechanisms of action, in which they may, as in USP4, or may not, as in USP7, use the direct resemblance to ubiquitin.

Tunable assembly of biomimetic peptoids as templates to control nanostructure catalytic activity

Nanoscale ◽  
2018 ◽  
Vol 10 (26) ◽  
pp. 12445-12452 ◽  
Author(s):  
Nicholas A. Merrill ◽  
Feng Yan ◽  
Haibao Jin ◽  
Peng Mu ◽  
Chun-Long Chen ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Structure And Function ◽  
And Function

Tunable peptoid assembly directs the control over structure and function of Pd nanomaterial catalysts.

The Molecular Mechanism of Photoinhibition — Facts and Fiction

1988 ◽  
Vol 15 (2) ◽  
pp. 27 ◽  
Author(s):  
C Critchley
Keyword(s):  
Photosystem Ii ◽  
Molecular Mechanism ◽  
Functional Group ◽  
Structure And Function ◽  
The Other ◽  
Proteolytic Degradation ◽  
Reaction Centre ◽  
Herbicide Binding ◽  
Recent Developments ◽  
And Function

In this paper, the evidence supporting two different models for the molecular mechanism of photoinhibition is discussed. One hypothesis centres around the suggestion that photoinhibition is due to the loss of the herbicide-binding Dl polypeptide of photosystem II. The other model suggests that damage to a functional group in the reaction centre is the primary cause of photoinhibition. In order to put the apparent controversy into context, recent developments in our understanding of the structure and function of the photosystem II reaction centre are described. Interpretation and judgement of all available evidence suggest primary photoinhibitory damage to be incurred by the reaction-centre chlorophyll P680 destabilising the apoprotein(s) and eventually resulting in their proteolytic degradation and removal from the photosystem II complex and the thylakoid membrane.

scholarly journals The Progress of Mitophagy and Related Pathogenic Mechanisms of the Neurodegenerative Diseases and Tumor

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Ying Song ◽  
Wei Ding ◽  
Yan Xiao ◽  
Kong-jun Lu
Keyword(s):  
Neurodegenerative Diseases ◽  
Molecular Mechanism ◽  
Normal State ◽  
Mitochondrial Membrane ◽  
Eukaryotic Cell ◽  
Signal Pathway ◽  
Structure And Function ◽  
Regulation Mechanism ◽  
Energy Center ◽  
And Function

Mitochondrion, an organelle with two layers of membrane, is extremely vital to eukaryotic cell. Its major functions are energy center and apoptosis censor inside cell. The intactness of mitochondrial membrane is important to maintain its structure and function. Mitophagy is one kind of autophagy. In recent years, studies of mitochondria have shown that mitophagy is regulated by various factors and is an important regulation mechanism for organisms to maintain their normal state. In addition, abnormal mitophagy is closely related to several neurodegenerative diseases and tumor. However, the related signal pathway and its regulation mechanism still remain unclear. As a result, summarizing the progress of mitophagy and its related pathogenic mechanism not only helps to reveal the complicated molecular mechanism, but also helps to find a new target to treat the related diseases.

scholarly journals Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1

2010 ◽  
Vol 39 (1) ◽  
pp. 313-324 ◽  
Author(s):  
Mathieu Rappas ◽  
Antony W. Oliver ◽  
Laurence H. Pearl
Keyword(s):  
Dna Damage ◽  
Structure And Function ◽  
Dna Damage Checkpoint ◽  
Binding Region ◽  
And Function

Introductory Remarks

1981 ◽  
Vol 293 (1063) ◽  
pp. 3-4 ◽  
Keyword(s):  
Catalytic Activity ◽  
Natural Selection ◽  
Structure And Function ◽  
Competitive Environment ◽  
Recent Experience ◽  
Anaerobic Conditions ◽  
Structure Activity ◽  
Evolution By Natural Selection ◽  
And Function ◽  
Regulatory Properties

The three aspects of the enzymes of glycolysis - structure, activity and evolution - are, of course, closely interlinked, because catalytic activity, as well as regulatory properties, depend on structure. As for evolution, a relevant general principle of evolution by natural selection states that the chances of survival in a competitive environment are greatest if optimal use is made of resources. From this principle arises the question: are the structures of enzymes optimal or can more effective enzymes be visualized? In attempting to answer this question one must bear in mind that the main physiological significance of glycolysis is to, provide energy under anaerobic conditions. To make clear what I have in mind about the relations between evolution, structure and function, I should like to illustrate my point by a recent experience in a neighbouring field, that of aerobic energy-providing processes.

scholarly journals Activity and Affinity of Pin1 Variants

2019 ◽  
Author(s):  
Alexandra Born ◽  
Morkos A. Henen ◽  
Beat Vögeli
Keyword(s):  
Catalytic Activity ◽  
Ligand Binding ◽  
Binding Site ◽  
Structure And Function ◽  
Ligand Binding Site ◽  
Prolyl Isomerase ◽  
Peptidyl Prolyl Isomerase ◽  
Isomerase Activity ◽  
Ppiase Domain ◽  
And Function

Pin1 is a peptidyl-prolyl isomerase responsible for isomerizing phosphorylated S/T-P motifs. Pin1 has two domains that each have a distinct ligand binding site, but only its PPIase domain has catalytic activity. Vast evidence supports interdomain allostery of Pin1, with binding of a ligand to its regulatory WW domain impacting activity in the PPIase domain. Many diverse studies have made mutations in Pin1 in order to elucidate interactions that are responsible for ligand binding, isomerase activity, and interdomain allostery. Here, we summarize these mutations and their impact on Pin1’s structure and function.

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