scholarly journals Structure-Function and Industrial Relevance of Bacterial Aminopeptidase P

Catalysts ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1157
Author(s):  
Muhamad Nadzmi Omar ◽  
Raja Noor Zaliha Raja Abd Rahman ◽  
Noor Dina Muhd Noor ◽  
Wahhida Latip ◽  
Victor Feizal Knight ◽  
...  
Keyword(s):  
Metal Ion ◽  
Catalytic Mechanism ◽  
Structure And Function ◽  
Structural Basis ◽  
Methionine Aminopeptidase ◽  
Terminal Amino ◽  
Aminopeptidase P ◽  
And Function ◽  
Pita Bread ◽  
Industrial Relevance

Aminopeptidase P (APPro, E.C 3.4.11.9) cleaves N-terminal amino acids from peptides and proteins where the penultimate residue is proline. This metal-ion-dependent enzyme shares a similar fold, catalytic mechanism, and substrate specificity with methionine aminopeptidase and prolidase. It adopts a canonical pita bread fold that serves as a structural basis for the metal-dependent catalysis and assembles as a tetramer in crystals. Similar to other metalloaminopeptidase, APPro requires metal ions for its maximal enzymatic activity, with manganese being the most preferred cation. Microbial aminopeptidase possesses unique characteristics compared with aminopeptidase from other sources, making it a great industrial enzyme for various applications. This review provides a summary of recent progress in the study of the structure and function of aminopeptidase P and describes its various applications in different industries as well as its significance in the environment.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

scholarly journals Understanding the impacts of self-shuffling approach on structure and function of shuffled endoglucanase enzyme via MD simulations

2020 ◽  
Vol 45 (2) ◽  
Author(s):  
Aslı Yenenler ◽  
Umut Gerlevik ◽  
Ugur Sezerman
Keyword(s):  
Experimental Studies ◽  
Salt Bridge ◽  
Md Simulations ◽  
Structure And Function ◽  
Computational Approach ◽  
Intramolecular Interactions ◽  
Structural Basis ◽  
Functional Differences ◽  
Structural Differences ◽  
And Function

AbstractObjectiveWe identify the impacts of structural differences on functionality of EG3_S2 endoglucanase enzyme with MD studies. The results of previous experimental studies have been explained in details with computational approach. The objective of this study is to explain the functional differences between shuffled enzyme (EG3_S2) and its native counterpart (EG3_nat) from Trichoderma reseei, via Molecular Dynamics approach.Materials and methodsFor this purpose, we performed MD simulations along 30 ns at three different reaction temperatures collected as NpT ensemble, and then monitored the backbone motion, flexibilities of residues, and intramolecular interactions of EG3_S2 and EG3_nat enzymes.ResultsAccording to MD results, we conclude that EG3_S2 and EG3_nat enzymes have unique RMSD patterns, e.g. RMSD pattern of EG3_S2 is more dynamic than that of EG3_nat at all temperatures. In addition to this dynamicity, EG3_S2 establishes more salt bridge interactions than EG3_nat.ConclusionBy taking these results into an account with the preservation of catalytic Glu residues in a proper manner, we explain the structural basis of differences between shuffled and native enzyme via molecular dynamic studies.

scholarly journals Structural Basis of Redox Signaling in Photosynthesis: Structure and Function of Ferredoxin:thioredoxin Reductase and Target Enzymes

2004 ◽  
Vol 79 (3) ◽  
pp. 233-248 ◽  
Author(s):  
Shaodong Dai ◽  
Kenth Johansson ◽  
Myroslawa Miginiac-Maslow ◽  
Peter Schürmann ◽  
Hans Eklund
Keyword(s):  
Redox Signaling ◽  
Structure And Function ◽  
Structural Basis ◽  
And Function ◽  
Ferredoxin:Thioredoxin Reductase

The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism

Biochemistry ◽  
2016 ◽  
Vol 55 (46) ◽  
pp. 6421-6432 ◽  
Author(s):  
Laura Cendron ◽  
Ileana Ramazzina ◽  
Vincenzo Puggioni ◽  
Eleonora Maccacaro ◽  
Anastasia Liuzzi ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Structure And Function ◽  
And Function

scholarly journals Structural Basis for Metal Ion Coordination and the Catalytic Mechanism of Sphingomyelinases D

2005 ◽  
Vol 280 (14) ◽  
pp. 13658-13664 ◽  
Author(s):  
Mário T. Murakami ◽  
Matheus F. Fernandes-Pedrosa ◽  
Denise V. Tambourgi ◽  
Raghuvir K. Arni
Keyword(s):  
Metal Ion ◽  
Catalytic Mechanism ◽  
Structural Basis

A replicative and synthetic chromosomal unit-the modern concept of the chromomere

1966 ◽  
Vol 164 (995) ◽  
pp. 279-289 ◽  
Keyword(s):  
Molecular Level ◽  
Structure And Function ◽  
Structural Basis ◽  
Modern Concept ◽  
Chromosomal Structure ◽  
New Approaches ◽  
Combined Use ◽  
And Function

present-day discussions on chromosomal structure and function the old term chromomere’ (Fol 1891) is seldom mentioned and it may be debated whether at is still desirable to use such a term. Conventionally it describes the bead-like concentrations of chromatin linearly arranged along the chromosomal thread, without implications as to the structural basis of such a discontinuity. Two alternative interpretations of the chromomeric organization of the chromosome have been suggested, one in which the chromomeres were regarded as definite chromosomal bodies, different from the interchromomeric regions of the chromosome, and one which considered the chromomeres as structures resulting only from the local coiling of a continuous chromosomal thread. Neither the chromomere hypothesis (Belling 1928; Bridges 1935; Pontecorvo 1944) nor the chromonema hypothesis (Ris 1945) has been finally and universally accepted. This is because the morphological and cytogenetical evidence previously available was insufficient to extend our knowledge of chromosomal structure down to the molecular level. New approaches in this direction have recently been made by the combined use of cytological, autoradiographic and photometric methods. They draw new attention to the chromomere.

scholarly journals Computational Modeling of Claudin Structure and Function

2020 ◽  
Vol 21 (3) ◽  
pp. 742 ◽  
Author(s):  
Shadi Fuladi ◽  
Ridaka-Wal Jannat ◽  
Le Shen ◽  
Christopher R. Weber ◽  
Fatemeh Khalili-Araghi
Keyword(s):  
Small Molecules ◽  
Tight Junctions ◽  
Barrier Function ◽  
Functional Model ◽  
Structure And Function ◽  
Structural Basis ◽  
Crystallographic Structure ◽  
Epithelial Barrier Function ◽  
Transport Of Ions ◽  
And Function

Tight junctions form a barrier to control passive transport of ions and small molecules across epithelia and endothelia. In addition to forming a barrier, some of claudins control transport properties of tight junctions by forming charge- and size-selective ion channels. It has been suggested claudin monomers can form or incorporate into tight junction strands to form channels. Resolving the crystallographic structure of several claudins in recent years has provided an opportunity to examine structural basis of claudins in tight junctions. Computational and theoretical modeling relying on atomic description of the pore have contributed significantly to our understanding of claudin pores and paracellular transport. In this paper, we review recent computational and mathematical modeling of claudin barrier function. We focus on dynamic modeling of global epithelial barrier function as a function of claudin pores and molecular dynamics studies of claudins leading to a functional model of claudin channels.

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