Inference of Macromolecular Assemblies from Crystalline State

Krissinel, Eugene; Henrick, Kim

doi:10.1016/j.jmb.2007.05.022

Cited by 8,678 publications

(8,283 citation statements)

References 111 publications

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“…Furthermore, there are two hydrogen bond pairs at the Fas1-2 and FEI1 interface, reported in Table 1. The PDBePISA webserver 19 was used to obtain the solvation free energy gain upon interface formation (Δ i G, in kcal/mol) reported in Table 2 along with the accessible and buried surface area of the interface. It can be seen from Table 2 that the Fas1-2 Domain and FEI1 interface has higher accessible surface area, which is an important structural characteristic during the formation of the protein-protein interaction.…”

Section: Resultsmentioning

confidence: 99%

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

Turupcu

Almohamed

Oostenbrink

et al. 2018

Plant Signaling & Behavior

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The Arabidopsis thaliana Fasciclin like arabinogalactan protein 4 (FLA4) locus is required for normal root growth in a linear genetic pathway with the FEI1 and FEI2 loci coding for receptor-like kinases. The two Fas1 domains of FLA4 are conserved among angiosperms but only the C-terminal Fas1 domain is required for genetic function. We show that at low salt deletion of the N-terminal Fas1 domain of transgenic FLA4 leads to enhanced root elongation compared to the tandem Fas1 wild type version. Modeling the hypothetical interaction between FLA4 and FEI1 we show that the predicted interaction is predominantly involving the C-terminal Fas1 domain. Relative conformational mobility between the two FLA4 Fas1 domains might regulate the interaction with the FEI receptor kinases. We therefore speculate that the FLA4 FEI complex might be a sensor for environmental conditions in the apoplast.

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Section: Resultsmentioning

confidence: 99%

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

Turupcu

Almohamed

Oostenbrink

et al. 2018

Plant Signaling & Behavior

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“…Gel filtration chromatography and analysis by the PISA server 22 suggest that the biological unit of PonA1 is a monomer (data not shown). Crystallized PonA1 molecules (residues 249–643) contain the transpeptidase domain and one small adjacent domain at the N terminus of the transpeptidase domain (Figs 1A and 2).…”

Section: Resultsmentioning

confidence: 97%

Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin‐binding protein PonA1 reveal potential mechanisms of antibiotic resistance

et al. 2016

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Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic‐resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin‐binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor‐free form and in complex with penicillin V are reported. We used site‐directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β‐lactams. Structural comparison of the PonA1 apo‐form and the antibiotic‐bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4′‐α3 surrounding the penicillin‐binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β‐lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall‐targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections.DatabaseStructural data are available in the PDB database under the accession numbers 5CRF and 5CXW.

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“…1B), despite the full AccA3‐AccD6 dodecameric complex being used for crystallization. The dimerization interface has an area of ~ 1200 Å 2 per monomer, burying some 8% of the total surface area of the dimer as calculated by PISA 36. Interestingly, the PISA analysis of the dimer interface does not suggest the formation of stable quaternary structures in solution.…”

Section: Resultsmentioning

confidence: 98%

Crystal structure of the essential biotin‐dependent carboxylase AccA3 from Mycobacterium tuberculosis

Bennett

Högbom

2017

FEBS Open Bio

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Biotin‐dependent acetyl‐CoA carboxylases catalyze the committed step in type II fatty acid biosynthesis, the main route for production of membrane phospholipids in bacteria, and are considered a key target for antibacterial drug discovery. Here we describe the first structure of AccA3, an essential component of the acetyl‐CoA carboxylase system in Mycobacterium tuberculosis (MTb). The structure, sequence comparisons, and modeling of ligand‐bound states reveal that the ATP cosubstrate‐binding site shows distinct differences compared to other bacterial and eukaryotic biotin carboxylases, including all human homologs. This suggests the possibility to design MTb AccA3 subtype‐specific inhibitors. Database Coordinates and structure factors have been deposited in the Protein Data Bank with the accession number http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5MLK.

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Inference of Macromolecular Assemblies from Crystalline State

Cited by 8,678 publications

References 111 publications

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin‐binding protein PonA1 reveal potential mechanisms of antibiotic resistance

Crystal structure of the essential biotin‐dependent carboxylase AccA3 from Mycobacterium tuberculosis

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