4YLH
Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway
Summary for 4YLH
| Entry DOI | 10.2210/pdb4ylh/pdb |
| Related | 2NP9 2PG8 |
| Descriptor | DpgC, XENON, [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE, ... (4 entities in total) |
| Functional Keywords | dioxygenase, xe complex, hydrolase |
| Biological source | Streptomyces toyocaensis |
| Total number of polymer chains | 12 |
| Total formula weight | 592814.04 |
| Authors | Li, K.,Di Russo, N.V.,Condurso, H.L.,Roitberg, A.E.,Bruner, S.D. (deposition date: 2015-03-05, release date: 2015-08-05, Last modification date: 2023-09-27) |
| Primary citation | Di Russo, N.V.,Condurso, H.L.,Li, K.,Bruner, S.D.,Roitberg, A.E. Oxygen diffusion pathways in a cofactor-independent dioxygenase. Chem Sci, 6:6341-6348, 2015 Cited by PubMed Abstract: 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 O diffusion is emerging, where specific channels guide O 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 O 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 O 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 O in the absence of cofactors or metals, the way O reaches the active site is similar to that reported for other O-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 O access that are conserved among very different types of proteins. PubMed: 26508997DOI: 10.1039/C5SC01638J PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.58 Å) |
Structure validation
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