The structure and function of HPr

1998 ◽  
Vol 76 (2-3) ◽  
pp. 359-367 ◽  
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.

Depletion and Reconstitution of Active E. Coli Ribosomes

1975 ◽  
Vol 33 ◽  
pp. 640-641
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Protein Biosynthesis ◽  
Large Subunit ◽  
High Resolution Electron Microscopy ◽  
Small Subunit ◽  
Structure And Function ◽  
Biologically Active ◽  
Biological Macromolecules ◽  
E Coli ◽  
Resolution Electron ◽  
And Function

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.

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

2005 ◽  
Vol 73 (10) ◽  
pp. 6332-6339 ◽  
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.

scholarly journals Structure and function of proteins of the phosphotransferase system and of 6-phospho-β-glycosidases in Gram-positive bacteria

1993 ◽  
Vol 12 (1-3) ◽  
pp. 149-163 ◽  
Author(s):  
Wolfgang Hengstenberg ◽  
Detlef Kohlbrecher ◽  
Ellen Witt ◽  
Regina Kruse ◽  
Ingo Christiansen ◽  
...  
Keyword(s):  
Structure And Function ◽  
Phosphotransferase System ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
And Function

scholarly journals PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide–dependent biofilm formation

2020 ◽  
Vol 295 (34) ◽  
pp. 11949-11962 ◽  
Author(s):  
Lindsey S. Marmont ◽  
Gregory B. Whitfield ◽  
Roland Pfoh ◽  
Rohan J. Williams ◽  
Trevor E. Randall ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Biofilm Formation ◽  
Potential Role ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Structure And Function ◽  
Bacterial Polysaccharide ◽  
H Nmr ◽  
Short Chain Dehydrogenase ◽  
And Function

Pel is a GalNAc-rich bacterial polysaccharide that contributes to the structure and function of Pseudomonas aeruginosa biofilms. The pelABCDEFG operon is highly conserved among diverse bacterial species, and Pel may therefore be a widespread biofilm determinant. Previous annotation of pel gene clusters has helped us identify an additional gene, pelX, that is present adjacent to pelABCDEFG in >100 different bacterial species. The pelX gene is predicted to encode a member of the short-chain dehydrogenase/reductase (SDR) superfamily, but its potential role in Pel-dependent biofilm formation is unknown. Herein, we have used Pseudomonas protegens Pf-5 as a model to elucidate PelX function as Pseudomonas aeruginosa lacks a pelX homologue in its pel gene cluster. We found that P. protegens forms Pel-dependent biofilms; however, despite expression of pelX under these conditions, biofilm formation was unaffected in a ΔpelX strain. This observation led us to identify a pelX paralogue, PFL_5533, which we designate here PgnE, that appears to be functionally redundant to pelX. In line with this, a ΔpelX ΔpgnE double mutant was substantially impaired in its ability to form Pel-dependent biofilms. To understand the molecular basis for this observation, we determined the structure of PelX to 2.1 Å resolution. The structure revealed that PelX resembles UDP-GlcNAc C4-epimerases. Using 1H NMR analysis, we show that PelX catalyzes the epimerization between UDP-GlcNAc and UDP-GalNAc. Our results indicate that Pel-dependent biofilm formation requires a UDP-GlcNAc C4-epimerase that generates the UDP-GalNAc precursors required by the Pel synthase machinery for polymer production.

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

2000 ◽  
Vol 44 (1) ◽  
pp. 263-264
Author(s):  
K. Hanawa ◽  
S. Lee ◽  
H. Himeno ◽  
A. Muto
Keyword(s):  
Structure And Function ◽  
E Coli ◽  
And Function

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

2014 ◽  
Vol 33 (2) ◽  
pp. 143-149 ◽  
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

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

1994 ◽  
Vol 726 (1 DNA Damage) ◽  
pp. 223-235 ◽  
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

scholarly journals Crystal Structures of Escherichia coli ATP-Dependent Glucokinase and Its Complex with Glucose

2004 ◽  
Vol 186 (20) ◽  
pp. 6915-6927 ◽  
Author(s):  
Vladimir V. Lunin ◽  
Yunge Li ◽  
Joseph D. Schrag ◽  
Pietro Iannuzzi ◽  
Miroslaw Cygler ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Nucleophilic Attack ◽  
Phosphoryl Group ◽  
Amino Acid Residues ◽  
Phosphotransferase System ◽  
E Coli ◽  
Glucose Binding

ABSTRACT Intracellular glucose in Escherichia coli cells imported by phosphoenolpyruvate-dependent phosphotransferase system-independent uptake is phosphorylated by glucokinase by using ATP to yield glucose-6-phosphate. Glucokinases (EC 2.7.1.2) are functionally distinct from hexokinases (EC 2.7.1.1) with respect to their narrow specificity for glucose as a substrate. While structural information is available for ADP-dependent glucokinases from Archaea, no structural information exists for the large sequence family of eubacterial ATP-dependent glucokinases. Here we report the first structure determination of a microbial ATP-dependent glucokinase, that from E. coli O157:H7. The crystal structure of E. coli glucokinase has been determined to a 2.3-Å resolution (apo form) and refined to final R work/R free factors of 0.200/0.271 and to 2.2-Å resolution (glucose complex) with final R work/R free factors of 0.193/0.265. E. coli GlK is a homodimer of 321 amino acid residues. Each monomer folds into two domains, a small α/β domain (residues 2 to 110 and 301 to 321) and a larger α+β domain (residues 111 to 300). The active site is situated in a deep cleft between the two domains. E. coli GlK is structurally similar to Saccharomyces cerevisiae hexokinase and human brain hexokinase I but is distinct from the ADP-dependent GlKs. Bound glucose forms hydrogen bonds with the residues Asn99, Asp100, Glu157, His160, and Glu187, all of which, except His160, are structurally conserved in human hexokinase 1. Glucose binding results in a closure of the small domains, with a maximal Cα shift of ∼10 Å. A catalytic mechanism is proposed that is consistent with Asp100 functioning as the general base, abstracting a proton from the O6 hydroxyl of glucose, followed by nucleophilic attack at the γ-phosphoryl group of ATP, yielding glucose-6-phosphate as the product.

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