scholarly journals Crystal Structure of DsbA from Corynebacterium diphtheriae and Its Functional Implications for CueP in Gram-Positive Bacteria

2015 ◽  
Vol 38 (8) ◽  
pp. 715-722 ◽  
Author(s):  
Si-Hyeon Um ◽  
Jin-Sik Kim ◽  
Saemee Song ◽  
Nam Ah Kim ◽  
Seong Hoon Jeong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Corynebacterium Diphtheriae ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Functional Implications

scholarly journals Crystal structure of human peptidoglycan recognition protein Iα bound to a muramyl pentapeptide from Gram-positive bacteria

2006 ◽  
Vol 15 (5) ◽  
pp. 1199-1206 ◽  
Author(s):  
Rongjin Guan ◽  
Patrick H. Brown ◽  
Chittoor P. Swaminathan ◽  
Abhijit Roychowdhury ◽  
Geert-Jan Boons ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Gram Positive ◽  
Peptidoglycan Recognition Protein ◽  
Gram Positive Bacteria ◽  
Recognition Protein

Crystal structure of a peptidoglycan recognition protein (PGRP) in complex with a muramyl tripeptide from Gram-positive bacteria

2005 ◽  
Vol 11 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Rongjin Guan ◽  
Abhijit Roychowdury ◽  
Brian Ember ◽  
Sanjay Kumar ◽  
Geert-Jan Boons ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Gram Positive ◽  
Peptidoglycan Recognition Protein ◽  
Gram Positive Bacteria ◽  
Recognition Protein

scholarly journals Sortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanism

2021 ◽  
Vol 118 (12) ◽  
pp. e2019649118
Author(s):  
Scott A. McConnell ◽  
Rachel A. McAllister ◽  
Brendan R. Amer ◽  
Brendan J. Mahoney ◽  
Christopher K. Sue ◽  
...  
Keyword(s):  
Solution Structure ◽  
Corynebacterium Diphtheriae ◽  
Crosslinking Reaction ◽  
Gram Positive ◽  
Kinetic Measurements ◽  
Sorting Signal ◽  
Gram Positive Bacteria ◽  
Isopeptide Bond ◽  
Assembly Mechanism ◽  
Binding Groove

Gram-positive bacteria assemble pili (fimbriae) on their surfaces to adhere to host tissues and to promote polymicrobial interactions. These hair-like structures, although very thin (1 to 5 nm), exhibit impressive tensile strengths because their protein components (pilins) are covalently crosslinked together via lysine–isopeptide bonds by pilus-specific sortase enzymes. While atomic structures of isolated pilins have been determined, how they are joined together by sortases and how these interpilin crosslinks stabilize pilus structure are poorly understood. Using a reconstituted pilus assembly system and hybrid structural biology methods, we elucidated the solution structure and dynamics of the crosslinked interface that is repeated to build the prototypical SpaA pilus from Corynebacterium diphtheriae. We show that sortase-catalyzed introduction of a K190-T494 isopeptide bond between adjacent SpaA pilins causes them to form a rigid interface in which the LPLTG sorting signal is inserted into a large binding groove. Cellular and quantitative kinetic measurements of the crosslinking reaction shed light onto the mechanism of pilus biogenesis. We propose that the pilus-specific sortase in C. diphtheriae uses a latch mechanism to select K190 on SpaA for crosslinking in which the sorting signal is partially transferred from the enzyme to a binding groove in SpaA in order to facilitate catalysis. This process is facilitated by a conserved loop in SpaA, which after crosslinking forms a stabilizing latch that covers the K190-T494 isopeptide bond. General features of the structure and sortase-catalyzed assembly mechanism of the SpaA pilus are likely conserved in Gram-positive bacteria.

scholarly journals Crystal structure of a peptidoglycan recognition protein (PGRP) in complex with a muramyl tripeptide from Gram-positive bacteria

2005 ◽  
Vol 11 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Rongjin Guan ◽  
Abhijit Roychowdury ◽  
Brian Ember ◽  
Sanjay Kumar ◽  
Geert-Jan Boons ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Gram Positive ◽  
Peptidoglycan Recognition Protein ◽  
Gram Positive Bacteria ◽  
Recognition Protein

scholarly journals A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease

IUCrJ ◽  
2020 ◽  
Vol 7 (3) ◽  
pp. 509-521
Author(s):  
Kyu-Yeon Lee ◽  
Seung-Ho Cheon ◽  
Dong-Gyun Kim ◽  
Sang Jae Lee ◽  
Bong-Jin Lee
Keyword(s):  
Crystal Structure ◽  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Catalytic Mechanism ◽  
Nuclease Activity ◽  
Binding Mode ◽  
Functional Study ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Key Residues

TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium Staphylococcus aureus (SaTatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although SaTatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of SaTatD revealed a unique binding mode of two phosphates interacting with two Ni2+ ions. Through a functional study, it was verified that SaTatD has Mg2+-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni2+ ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of SaTatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by SaTatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of SaTatD was proposed using in silico docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of SaTatD.

Crystal structure and functional implications of LprF fromMycobacterium tuberculosisandM. bovis

2014 ◽  
Vol 70 (10) ◽  
pp. 2619-2630 ◽  
Author(s):  
Jin-Sik Kim ◽  
Li Jiao ◽  
Jeong-Il Oh ◽  
Nam-Chul Ha ◽  
Yong-Hak Kim
Keyword(s):  
Crystal Structure ◽  
Cell Wall ◽  
Spectrometric Analysis ◽  
Alkyl Chains ◽  
Gram Positive Bacteria ◽  
Cavity Structure ◽  
Functional Implications ◽  
Causative Agents ◽  
Mycobacterial Cell Wall

The Gram-positive bacteriaMycobacterium tuberculosisandM. bovisare causative agents of tuberculosis in humans and cattle. The lipoprotein LprF is found inM. tuberculosisandM. bovisbut not in the nonpathogenicM. smegmatis. To date, the role of LprF remains to be elucidated. In this study, the crystal structure of LprF has been determined at 1.1 Å resolution. The overall structure is similar to that of a homologue, LprG, with a central hydrophobic cavity that binds a triacylated glycolipid. LprF exhibited a central cavity structure similar to that of LprG, but with a smaller cavity that binds two alkyl chains. Consistently, subsequent mass-spectrometric analysis revealed that the bound ligand was a diacylated glycolipid, as found in the structure. Furthermore, an increased ratio of lipoarabinomannan to lipomannan in the mycobacterial cell wall was observed whenlprFwas introduced intoM. smegmatis. These observations suggested that LprF transfers the diacylated glycolipid from the plasma membrane to the cell wall, which might be related to the pathogenesis of the bacteria.

scholarly journals Crystal Structure of AcrB Complexed with Linezolid at 3.5Å Resolution

2014 ◽  
Vol 70 (a1) ◽  
pp. C1493-C1493
Author(s):  
Li-Wei Hung ◽  
Heungbok Kim ◽  
Satoshi Murakami ◽  
Goutam Gupta ◽  
Chang-Yub Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Efflux Pump ◽  
Ribosomal Subunit ◽  
Membrane Resistance ◽  
Gram Positive ◽  
Gram Negative ◽  
E Coli ◽  
Gram Positive Bacteria ◽  
Resistance Nodulation Division ◽  
Clinically Significant

"We present the crystal structure of AcrB in complex with Linezolid[1]. AcrB is an inner-membrane Resistance-Nodulation-Division efflux pump and is part of the AcrAB-TolC multidrug-resistance tripartite efflux system in E. Coli. Crystal structures of AcrB by itself as well as several drug-bound complexes have been structurally characterized. Linezolid is an approved oxazolidinone antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to other antibiotics, and has been called a ""reserve antibiotic"", a drug of last resort against potentially intractable infections. This antibiotic inhibits bacterial protein synthesis by specifically binding to the 50S ribosomal subunit. Linezolid has no clinically significant effect on most Gram-negative bacteria. This is thought to be a result of relatively low intracellular concentration of Linezolid due to efflux, but there is no direct evidence yet to support this hypothesis. This membrane protein-drug complex shows that an antibiotic specific to Gram-positive bacteria can also bind an efflux pump from E. coli, a Gram-negative bacterium. The crystal structure of AcrB and Linezolid complex reveals that Linezolid binds to the A385/F386 loops of the symmetric trimers of AcrB in the same fashion as several other antibiotics that are extruded by efflux pumps. A conformational change of a loop in the bottom of the periplasmic cleft is also observed."

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