The dark and bright sides of an enzyme: a three dimensional structure of the N-terminal domain of Zophobas morio luciferase-like enzyme, inferences on the biological function and origin of oxygenase/luciferase activity

2016 ◽  
Vol 15 (5) ◽  
pp. 654-665 ◽  
Author(s):  
R. A. Prado ◽  
C. R. Santos ◽  
D. I. Kato ◽  
M. T. Murakami ◽  
V. R. Viviani
Keyword(s):  
Biological Function ◽  
Luciferase Activity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Catalytic Residue ◽  
Three Dimensional Structure ◽  
Catalytic Activities ◽  
Terminal Domain ◽  
Coa Ligase

The structure and catalytic activities of a Malpighian luciferase-like enzyme indicate a generalistic xenobiotic CoA-ligase and a catalytic residue for bioluminescence.

scholarly journals Three-dimensional structure of the amino-terminal domain of syntaxin 6, a SNAP-25 C homolog

2002 ◽  
Vol 99 (14) ◽  
pp. 9184-9189 ◽  
Author(s):  
K. M. S. Misura ◽  
J. B. Bock ◽  
L. C. Gonzalez ◽  
R. H. Scheller ◽  
W. I. Weis
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Amino Terminal ◽  
Terminal Domain ◽  
Amino Terminal Domain

scholarly journals Three-Dimensional Structure of N-Terminal Domain of DnaB Helicase and Helicase-Primase Interactions in Helicobacter pylori

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7515 ◽  
Author(s):  
Tara Kashav ◽  
Ramgopal Nitharwal ◽  
S. Arif Abdulrehman ◽  
Azat Gabdoulkhakov ◽  
Wolfram Saenger ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Terminal Domain ◽  
Dnab Helicase

scholarly journals Comparing the fluctuations of the intrinsically disordered C-terminal domain of human SELK free in water and in lipid membrane

2015 ◽  
Author(s):  
Andrea Polo ◽  
Stefano Guariniello ◽  
Giovanni Colonna ◽  
Gennaro Ciliberto ◽  
Susan Costantini
Keyword(s):  
Endoplasmic Reticulum ◽  
Ab Initio ◽  
Lipid Bilayer ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Interaction Data ◽  
Endoplasmic Reticulum Membrane ◽  
Three Dimensional Structure ◽  
Intrinsically Disordered ◽  
Terminal Domain

SELK is a single-pass trans-membrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is resulted to be up-expressed in hepatocellular carcinoma and in other cancers, therefore there is a need to analyze its structure-function relationships. In this work we performed a detailed analysis of the C-terminal domain sequence of SELK, modeled its three-dimensional structure and analyzed its conformational changes by Molecular Dynamics simulations. Our analysis showed that the C-terminal domain of SELK is a weak polyelectrolyte and specifically, a polycation, which has the characteristic molecular signature of natively disordered segments. Since the search by BLAST has not evidenced possible templates with an acceptable sequence identity percentage with the C-terminal sequence of SELK, its three-dimensional structure was modeled by ab initio modeling. The best model is characterized by one short helix and the most part of residues with no regular secondary structure elements. This model was subjected to MD simulation at neutral pH in water to assess the stability of the modelled structural organization free in solution. To deepen the structural analysis of the C terminal domain, we have also studied the organization of the whole protein inserted into the membrane by a procedure of comparative modeling between fold recognition and folding ab initio. Then, the complete structure of SELK was subjected to MD simulations in the lipid bilayer and a water box. Analyzing the MD trajectories, we found that the C-terminal domain of SELK is still highly mobile during the simulation in water-lipid bilayer by showing a decrease of the structural compactness, a lesser number of H-bonds, as well as a higher value of the total void volume and of the total solvent accessible area compared to the simulation in only water system. However, in both the simulations this region is stabilized mainly by a marked number of H-bonds, and pi-cation and IAC interactions, which suggest a globule organization very different from the classic globular one. Furthermore, water-protein interaction data suggest, as for other IDPs, that the hydration water tends to cluster around the protein facilitating its organization to globule.

Low-complexity sequences and single amino acid repeats: not just “junk” peptide sequences

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 753-762 ◽  
Author(s):  
Wilfried Haerty ◽  
G. Brian Golding
Keyword(s):  
Biological Function ◽  
Three Dimensional ◽  
Size Variation ◽  
Low Complexity ◽  
Single Amino Acid ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Amino Acid Repeats ◽  
Eukaryotic Proteomes ◽  
Definition Of

For decades proteins were thought to interact in a “lock and key” system, which led to the definition of a paradigm linking stable three-dimensional structure to biological function. As a consequence, any non-structured peptide was considered to be nonfunctional and to evolve neutrally. Surprisingly, the most commonly shared peptides between eukaryotic proteomes are low-complexity sequences that in most conditions do not present a stable three-dimensional structure. However, because these sequences evolve rapidly and because the size variation of a few of them can have deleterious effects, low-complexity sequences have been suggested to be the target of selection. Here we review evidence that supports the idea that these simple sequences should not be considered just “junk” peptides and that selection drives the evolution of many of them.

scholarly journals Three-Dimensional Structure of an Evolutionarily Conserved N-Terminal Domain of Syntaxin 1A

Cell ◽  
1998 ◽  
Vol 94 (6) ◽  
pp. 841-849 ◽  
Author(s):  
Imma Fernandez ◽  
Josep Ubach ◽  
Irina Dulubova ◽  
Xiangyang Zhang ◽  
Thomas C Südhof ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Syntaxin 1A ◽  
Three Dimensional Structure ◽  
Terminal Domain ◽  
Evolutionarily Conserved
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