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Figure 2 | BMC Structural Biology

Figure 2

From: Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases

Figure 2

Homology modeling of the R domain. (A) Multiple sequence alignment of the R domains within characterized proteins: Multiple sequence alignments of the R domains from the experimentally characterized NRPS/PKS clusters. Sequence information of the synsthases can be found at Figure 1B. The alignment showed that the NADPH binding site and the catalytic site (marked with black and green asterisks) are conserved. (B) Sequence alignment used to build the R domain model (glycopeptidolipid) based on the VR template retrieved by MOE. Gray blocks indicate the level of sequence similarity. Tallest blocks: residues are identical at that position. Intermediate blocks: residues are not identical but relatively similar based on their properties. Small blocks: residues are somewhat conserved with respect to structure or function. The absence of blocks indicates no appreciable structure/function conservation. Gaps in one sequence relative to the other are indicated by dashes. The UCSF chimera visualization system was used to generate this figure [64].

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