Structural basis for the peptidoglycan editing activity of YfiH

AbstractBacterial cells are encased in peptidoglycan (PG), a polymer of disaccharide N-acetyl-glucosamine (GlcNAc) and N-acetyl-muramic acid (MurNAc) cross-linked by peptide stems. PG is synthesized in the cytoplasm as UDP-MurNAc-peptide precursors, of which the amino-acid composition of the peptide is unique, with L-Ala added at the first position in most bacteria but L-Ser or Gly in some bacteria. YfiH is a PG-editing factor whose absence causes misincorporation of L-Ser instead of L-Ala into peptide stems; but its mechanistic function is unknown. Here we report the crystal structures of substrate-bound and product-bound YfiH, showing that YfiH is a cytoplasmic amidase that controls the incorporation of the correct amino acid to the nucleotide precursors by preferentially cleaving the nucleotide precursor byproduct UDP-MurNAc-L-Ser. This work reveals an editing mechanism in the cytoplasmic steps of peptidoglycan biosynthesis.

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The amino acid composition of mammalian and bacterial cells

Amino Acids ◽

10.1007/bf01372601 ◽

1997 ◽

Vol 13 (3-4) ◽

pp. 379-391 ◽

Cited By ~ 27

Author(s):

T. Okayasu ◽

M. Ikeda ◽

K. Akimoto ◽

K. Sorimachi

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Acid Composition ◽

Bacterial Cells

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Transformation of amino acid composition in bacterial cells of Lactobacillus bulgaricus during freeze-drying

Cryobiology ◽

10.1016/0011-2240(76)90135-8 ◽

1976 ◽

Vol 13 (2) ◽

pp. 214-217 ◽

Cited By ~ 3

Author(s):

Stojanka Mitić

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Acid Composition ◽

Freeze Drying ◽

Lactobacillus Bulgaricus ◽

Bacterial Cells

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Predicting the quaternary structure attribute of a protein by hybridizing functional domain composition and pseudo amino acid composition

Journal of Applied Crystallography ◽

10.1107/s0021889809002751 ◽

2009 ◽

Vol 42 (2) ◽

pp. 169-173 ◽

Cited By ~ 53

Author(s):

Xuan Xiao ◽

Pu Wang ◽

Kuo-Chen Chou

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Acid Composition ◽

Quaternary Structure ◽

Structural Basis ◽

Sequence Information ◽

Functional Domain ◽

Protein Chain ◽

Pseudo Amino Acid Composition ◽

Domain Composition

In vivo, some proteins exist as monomers (single polypeptide chains) and others as oligomers. The latter are composed of two or more chains (subunits) that are associated with each other through noncovalent interactions and, occasionally, disulfide bonds. Oligomers can be further classified into homo-oligomers (formed by identical subunits) and hetero-oligomers (formed by different subunits), and they form the structural basis of various biological functions such as cooperative effects, the allosteric mechanism and ion-channel gating. Therefore, it would be of less interest or of low priority for crystallographic scientists to crystallize a single protein chain and determine its three-dimensional structure if it is already known as part of an oligomer. However, it is both time-consuming and laborious to acquire such information on the quaternary structure attribute purely by experiment. In particular, with the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop an automated method by which crystallographic scientists can rapidly and effectively identify which quaternary attribute a particular protein chain has according to its sequence information. In view of this, a computational method has been developed by hybridizing the approaches of functional domain composition and pseudo amino acid composition. For the convenience of crystallographic scientists, a user-friendly web server,PQSA-Pred, has been established at http://218.65.61.89:8080/bioinfo/pqsa-pred, by which the desired information can be easily obtained.

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Analysis of Known Bacterial Protein Vaccine Antigens Reveals Biased Physical Properties and Amino Acid Composition

Comparative and Functional Genomics ◽

10.1002/cfg.319 ◽

2003 ◽

Vol 4 (5) ◽

pp. 468-478 ◽

Cited By ~ 15

Author(s):

Carl Mayers ◽

Melanie Duffield ◽

Sonya Rowe ◽

Julie Miller ◽

Bryan Lingard ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Acid Composition ◽

Pathogenic Bacteria ◽

Vaccine Antigen ◽

Bacterial Cells ◽

Protein Vaccine ◽

Vaccine Antigens ◽

Candidate Protein ◽

Potential Vaccine

Many vaccines have been developed from live attenuated forms of bacterial pathogens or from killed bacterial cells. However, an increased awareness of the potential for transient side-effects following vaccination has prompted an increased emphasis on the use of sub-unit vaccines, rather than those based on whole bacterial cells. The identification of vaccine sub-units is often a lengthy process and bioinformatics approaches have recently been used to identify candidate protein vaccine antigens. Such methods ultimately offer the promise of a more rapid advance towards preclinical studies with vaccines. We have compared the properties of known bacterial vaccine antigens against randomly selected proteins and identified differences in the make-up of these two groups. A computer algorithm that exploits these differences allows the identification of potential vaccine antigen candidates from pathogenic bacteria on the basis of their amino acid composition, a property inherently associated with sub-cellular location.

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CELL DIVISION IN A SPECIES OF ERWINIA: VIII. AMINO ACID COMPOSITION OF THE MUCOPEPTIDE IN DIVIDING AND NON-DIVIDING CELLS

Canadian Journal of Microbiology ◽

10.1139/m65-080 ◽

1965 ◽

Vol 11 (4) ◽

pp. 605-610 ◽

Cited By ~ 3

Author(s):

E. A. Grula ◽

Gerald L. Smith ◽

Mary M. Grula

Keyword(s):

Cell Division ◽

Amino Acid ◽

Amino Acid Composition ◽

Aspartic Acid ◽

Ammonium Chloride ◽

Acid Composition ◽

Defined Medium ◽

Muramic Acid ◽

Dividing Cells ◽

Positive Compound

The Erwinia sp. studied possesses a discrete mucopeptide layer. This layer contains glutamic, diaminopimelic, and muramic acid, glucosamine, and alanine (1–1–1–1–2) as major components. Aspartic acid, glycine, and an unidentified ninhydrin-positive compound are also present but in lesser amounts. Content of glycine increases when cells are grown in a defined medium in the presence of glycine. Serine is present in the mucopeptide when cells are grown in the presence of D-serine, an inhibitor of cell division. Serine can partially replace glycine. Incorporation of serine is not significantly decreased by agents capable of preventing division inhibition by D-serine (pantoyl lactone or ammonium chloride). A new method for isolation of pure mucopeptide is presented.

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