4ylh

Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway

spinqualitylabelsall models 4ylh, resolution 2.58Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4ylh is a 12 chain structure with sequence from Streptomyces toyocaensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.58Å Ligands: XE, YE1 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DPGC_STRTO Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875). Publication Abstract from PubMed Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O2 diffusion is emerging, where specific channels guide O2 to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O2 reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O2 at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O2 in the absence of cofactors or metals, the way O2 reaches the active site is similar to that reported for other O2-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O2 access that are conserved among very different types of proteins. Oxygen diffusion pathways in a cofactor-independent dioxygenase.,Di Russo NV, Condurso HL, Li K, Bruner SD, Roitberg AE Chem Sci. 2015 Nov 1;6(11):6341-6348. Epub 2015 Jul 23. PMID:26508997 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Enoyl-CoA hydratase 3D structures

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