6p9d | pdb_00006p9d

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with FAD - Yellow fraction

spinqualitylabelsall models 6p9d, resolution 1.33Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6p9d is a 1 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.329Å Ligands: FDA, GOL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DAUA_PSEAE DauA is highly expressed within the cystic fibrosis (CF) lung, and it is required for virulence via the optimal production of hydrogen cyanide, pyocyanine, pyoverdine, rhamnolipid and alginate during biofilm formation (PubMed:24011342). Involved in the catabolism of D-lysine and D-arginine. Under aerobic conditions, the arginine succinyltransferase (AST) and arginine transaminase (ATA) pathways are 2 major routes for L-arginine utilization as the sole source of carbon and nitrogen. The D-to-L racemization of arginine by DauA and DauB is necessary, before to be channeled into the AST and/or ATA pathways. DauA catalyzes the flavin-dependent oxidative deamination of D-arginine into 2-ketoarginine (2-KA) and ammonia (PubMed:3141581, PubMed:19139398, PubMed:19850617, PubMed:20809650). It has also dehydrogenase activity towards D-lysine, D-tyrosine, D-methionine, D-phenylalanine, D-ornithine, D-histidine and D-leucine as substrates (PubMed:19850617, PubMed:20809650). Publication Abstract from PubMed Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity.,Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G Biochemistry. 2021 Mar 9;60(9):711-724. doi: 10.1021/acs.biochem.1c00054. Epub, 2021 Feb 25. PMID:33630571 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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