The structure and function of tRNA-like domain in E. coli tmRNA

Correlations between structure and function of biological macromolecules have been studied intensively for many years, mostly by indirect methods. High resolution electron microscopy is a unique tool which can provide such information directly by comparing the conformation of biopolymers in their biologically active and inactive state. We have correlated the structure and function of ribosomes, ribonucleoprotein particles which are the site of protein biosynthesis. 70S E. coli ribosomes, used in this experiment, are composed of two subunits - large (50S) and small (30S). The large subunit consists of 34 proteins and two different ribonucleic acid molecules. The small subunit contains 21 proteins and one RNA molecule. All proteins (with the exception of L7 and L12) are present in one copy per ribosome.This study deals with the changes in the fine structure of E. coli ribosomes depleted of proteins L7 and L12. These proteins are unique in many aspects.

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Conserved Structure and Function in the Granulysin and NK-Lysin Peptide Family

Infection and Immunity ◽

10.1128/iai.73.10.6332-6339.2005 ◽

2005 ◽

Vol 73 (10) ◽

pp. 6332-6339 ◽

Cited By ~ 33

Author(s):

Charlotte M. A. Linde ◽

Susanna Grundström ◽

Erik Nordling ◽

Essam Refai ◽

Patrick J. Brennan ◽

...

Keyword(s):

Mycobacterium Smegmatis ◽

Three Dimensional ◽

Antimycobacterial Activity ◽

Structure And Function ◽

Loop Structure ◽

E Coli ◽

Short Loop ◽

Peptide Family ◽

And Function ◽

Related Proteins

ABSTRACT Granulysin and NK-lysin are homologous bactericidal proteins with a moderate residue identity (35%), both of which have antimycobacterial activity. Short loop peptides derived from the antimycobacterial domains of granulysin, NK-lysin, and a putative chicken NK-lysin were examined and shown to have comparable antimycobacterial but variable Escherichia coli activities. The known structure of the NK-lysin loop peptide was used to predict the structure of the equivalent peptides of granulysin and chicken NK-lysin by homology modeling. The last two adopted a secondary structure almost identical to that of NK-lysin. All three peptides form very similar three-dimensional (3-D) architectures in which the important basic residues assume the same positions in space. The basic residues in granulysin are arginine, while those in NK-lysin and chicken NK-lysin are a mixture of arginine and lysine. We altered the ratio of arginine to lysine in the granulysin fragment to examine the importance of basic residues for antimycobacterial activity. The alteration of the amino acids reduced the activity against E. coli to a larger extent than that against Mycobacterium smegmatis. In granulysin, the arginines in the loop structure are not crucial for antimycobacterial activity but are important for cytotoxicity. We suggest that the antibacterial domains of the related proteins granulysin, NK-lysin, and chicken NK-lysin have conserved their 3-D structure and their function against mycobacteria.

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Structure and Function of E. coli Formylmethionyl tRNA, I. Effect of Modification of Pyrimidine Residues on Aminoacyl Synthetase Recognition

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.66.2.507 ◽

1970 ◽

Vol 66 (2) ◽

pp. 507-514 ◽

Cited By ~ 24

Author(s):

L. H. Schulman

Keyword(s):

Structure And Function ◽

E Coli ◽

And Function

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Critical Role of Zinc Ion on E. coli Glutamyl-Queuosine-tRNAAsp Synthetase (Glu-Q-RS) Structure and Function

The Protein Journal ◽

10.1007/s10930-014-9546-1 ◽

2014 ◽

Vol 33 (2) ◽

pp. 143-149 ◽

Cited By ~ 2

Author(s):

Sutapa Ray ◽

Victor Banerjee ◽

Mickael Blaise ◽

Baisakhi Banerjee ◽

Kali Pada Das ◽

...

Keyword(s):

Critical Role ◽

Zinc Ion ◽

Structure And Function ◽

E Coli ◽

And Function

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The structure and function of HPr

Biochemistry and Cell Biology ◽

10.1139/o98-043 ◽

1998 ◽

Vol 76 (2-3) ◽

pp. 359-367 ◽

Cited By ~ 12

Author(s):

E Bruce Waygood

Keyword(s):

Structure And Function ◽

Side Chain ◽

Phosphoryl Group ◽

Phosphotransferase System ◽

Tertiary Structures ◽

E Coli ◽

H Nmr ◽

Early Protein ◽

Alpha Beta ◽

And Function

Histidine-containing phosphocarrier protein, HPr, was one of the early protein tertiary structures determined by two-dimensional 1H-NMR. Tertiary structures for HPrs from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus have been obtained by 1H NMR and the overall folding pattern of HPr is highly conserved, a beta alpha beta beta alpha beta alpha arrangement of three alpha-helices overlaying a four-stranded beta-sheet. High-resolution structures for HPrs from E. coli and B. subtilis have been obtained using 15N- and 13C-labeled proteins. The first application of NMR to the understanding of the structure and function of HPr was to describe the phosphohistidine isomer, Ndelta1-P-histidine in S. aureus phospho-HPr, and the unusual pKas of the His-15 side chain. The pKa values for the His-15 imidazole from more recent studies are 5.4 for HPr and 7.8 for phospho-HPr from E. coli, for example. A consensus description of the active site is proposed for HPr and phospho-HPr. In HPr, His-15 has a defined conformation and N-caps helix A, and is thus affected by the helix dipole. His-15 undergoes a small conformational change upon phosphorylation, a movement to allow the phosphoryl group to be positioned such that it forms hydrogen bonds with the main chain amide nitrogens of residue 16 (not conserved) and Arg-17. Interactions between residue 12 side chain (not conserved: asparagine, serine, and threonine) and His-15, and between the Arg-17 guanidinium group and the phosphoryl group, are either weak or transitory.Key words: HPr, NMR, phosphoenolpyruvate:sugar phosphotransferase system, phosphohistidine, phosphoserine.

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Structure and Function of the DNA Repair Enzyme Exonuclease III from E. Coli

Annals of the New York Academy of Sciences ◽

10.1111/j.1749-6632.1994.tb52820.x ◽

1994 ◽

Vol 726 (1 DNA Damage) ◽

pp. 223-235 ◽

Cited By ~ 13

Author(s):

CHE-FU KUO ◽

CLIFFORD D. MOL ◽

MARIA M. THAYER ◽

RICHARD P. CUNNINGHAM ◽

JOHN A. TAINERC

Keyword(s):

Dna Repair ◽

Structure And Function ◽

Repair Enzyme ◽

Exonuclease Iii ◽

E Coli ◽

And Function

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Correlating the structure and activity of Y. pestis Ail in a bacterial cell envelope

10.1101/2020.09.23.310672 ◽

2020 ◽

Author(s):

J. E. Kent ◽

L. M. Fujimoto ◽

K. Shin ◽

C. Singh ◽

Y. Yao ◽

...

Keyword(s):

Immune Response ◽

Human Serum ◽

Bacterial Cell ◽

Model System ◽

Structure And Function ◽

Cell Surface Expression ◽

Therapeutic Drug ◽

E Coli ◽

Cell Envelopes ◽

And Function

ABSTRACTUnderstanding microbe-host interactions at the molecular level is a major goal of fundamental biology and therapeutic drug development. Structural biology strives to capture biomolecular structures in action, but the samples are often highly simplified versions of the complex native environment. Here we present an E. coli model system that allows us to probe the structure and function of Ail, the major surface protein of the deadly pathogen Yersinia pestis. We show that cell surface expression of Ail produces Y. pestis virulence phenotypes in E. coli, including resistance to human serum, co-sedimentation of human vitronectin and pellicle formation. Moreover, isolated bacterial cell envelopes, encompassing inner and outer membranes, yield high-resolution solid-state nuclear magnetic resonance (NMR) spectra that reflect the structure of Ail and reveal Ail sites that are sensitive to the bacterial membrane environment and involved in the interactions with human serum components. The data capture the structure and function of Ail in a bacterial outer membrane and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum.SIGNIFICANCEAil is a critical virulence factor of Y. pestis, and its interactions with human serum are central for promoting the immune resistance of bacteria to the human host defenses. Here we capture the action of Ail in a functional bacterial environment and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum. The development of an E. coli model system of Y. pestis for biophysical studies is new and biologically important. Finally, the work extends the range in-situ NMR spectroscopy to include models of microbial infection.

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Structural analysis of the E. coli RUVB branch migration protein by EM and image analysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100169419 ◽

1994 ◽

Vol 52 ◽

pp. 336-337

Author(s):

X. Yu ◽

K. Benson ◽

A. Stasiak ◽

I. Tsaneva ◽

S. West ◽

...

Keyword(s):

Image Analysis ◽

Atp Hydrolysis ◽

Genetic Recombination ◽

Sos Response ◽

Structure And Function ◽

Holliday Junctions ◽

Branch Migration ◽

E Coli ◽

Form Part ◽

And Function

We have been interested in the structure and function of proteins involved in genetic recombinaton. The ruv locus on the E. coli chromosome contains three genes (ruvA, ruvB and ruvC) that are important for genetic recombination and DNA repair. The ruvA and ruvB genes form part of the SOS response to DNA damage and encode the RuvA and RuvB proteins. Together, RuvA and RuvB promote the branch migration of Holliday junctions in a reaction that requires ATP hydrolysis. Each protein plays a defined role, with RuvA responsible for DNA binding (and, in particular, junction recognition), whereas the RuvB ATPase provides the motor for branch migration. Sequence analysis has identified RuvB as a member of a superfamily of helicases, and experimentally it has been shown that RuvB, in the presence of RuvA, acts as an ATP-dependent helicase.When purified RuvB protein was incubated (in the presence of the ATP analog, ATP-γ-S) with covalently closed, relaxed dsDNA, double-ringed structures were observed on the DNA in the electron microscope (Fig. 1). The DNA must be passing through the center of these rings, since the rings are always aligned along a common axis.

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Exogenous Production of N-acetylmuramyl-L Alanine Amidase (LysM2) from Siphoviridae Phage Affecting Anti-Gram-Negative Bacteria: Evaluation of Its Structure and Function

Avicenna Journal of Medical Biotechnology ◽

10.18502/ajmb.v14i1.8169 ◽

2022 ◽

Author(s):

Morteza Miri ◽

Sepideh Yazdianpour ◽

Shamsozoha Abolmaali ◽

Shakiba Darvish Alipour Astaneh

Keyword(s):

In Silico ◽

Alpha Helix ◽

Salmonella Typhi ◽

Structure And Function ◽

Gram Negative Bacteria ◽

Gene Encoding ◽

Gram Negative ◽

E Coli ◽

Antigenic Properties ◽

And Function

Background: To obtain endolysin with impact(s) on gram-negative bacteria as well as gram-positive bacteria, N-acetylmuramyl L-alanine-amidase (MurNAc-LAA) from a Bacillus subtilis-hosted Siphoviridae phage (SPP1 phage, Subtilis Phage Pavia 1) was exogenously expressed in Escherichia coli (E. coli). Methods: The sequences of MurNAc-LAA genes encoding peptidoglycan hydrolases were obtained from the Virus-Host database. The sequence of MurNAc-LAA was optimized by GenScript software to generate MurNAc-LAA-MMI (LysM2) for optimal expression in E. coli. Furthermore, the structure and function of LysM2 was evaluated in silico. The optimized gene was synthesized, subcloned in the pET28a, and expressed in E. coli BL21(DE3). The antibacterial effects of the protein on the peptidoglycan substrates were studied. Results: LysM2, on 816 bp gene encoding a 33 kDa protein was confirmed as specific SPP1 phage enzyme. The enzyme is composed of 271 amino acids, with a half-life of 10 hr in E. coli. In silico analyses showed 34.2% alpha-helix in the secondary structure, hydrophobic N-terminal, and lysine-rich C-terminal, and no antigenic properties in LysM2 protein. This optimized endolysin revealed impacts against Proteus (sp) by turbidity, and an antibacterial activity against Klebsiella pneumoniae, Salmonella typhi-murium, and Proteus vulgaris in agar diffusion assays. Conclusion: Taken together, our results confirmed that LysM2 is an inhibiting agent for gram-negative bacteria.

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