21JM
Crystal structure of high-molecular-weight PAH dihydrodiol dehydrogenase PahB from Altererythrobacter sp. H2 in complex with substrate
This is a non-PDB format compatible entry.
Summary for 21JM
| Entry DOI | 10.2210/pdb21jm/pdb |
| Descriptor | HMW-PAHs dihydrodiol dehydrogenase PahB, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, (1~{S},2~{R})-cyclohexa-3,5-diene-1,2-diol, ... (5 entities in total) |
| Functional Keywords | rossmann-like fold, nad-binding, aromatic compound degradation, dihydrodiol dehydrogenation, oxidoreductase |
| Biological source | Altererythrobacter sp. H2 |
| Total number of polymer chains | 1 |
| Total formula weight | 28859.40 |
| Authors | |
| Primary citation | Han, Q.,Tian, L.L.,Guo, L.,Cui, R.,Liu, Z.S.,Li, D.F. Structural and functional characterization of dihydrodiol dehydrogenase PahB recognizing high-molecular-weight PAH substrates. Appl.Environ.Microbiol., :e0012126-e0012126, 2026 Cited by PubMed Abstract: Polycyclic aromatic hydrocarbons (PAHs), especially high-molecular-weight PAHs (HMW-PAHs), are persistent environmental pollutants that are difficult to remove and challenge environmental management. sp. H2 degrades benzo[a]pyrene, benzo[a]anthracene, pyrene, fluoranthene, and phenanthrene, showing great potential in HMW-PAH removal. The aerobic degradation of HMW-PAHs by this strain is initiated by those well-studied ring-hydroxylating oxygenases, followed by subsequent dehydrogenation by less-studied dehydrogenases. Therefore, we investigated the substrate range and substrate recognition mechanism of dehydrogenase PahB from strain H2. Here, we found that PahB from sp. H2 can oxidize different HMW-PAH-derived dihydrodiols. Phylogenetic analysis showed that PahB belongs to the NahB-type branch, where it clusters with HMW-PAH-associated homologs, such as BphB-CHY-1, and remains distinct from biphenyl-type BphB dehydrogenases. Crystal structures and docking analyses revealed a hydrophobic, methionine-rich substrate-binding pocket that accommodates different HMW-PAH-derived dihydrodiols in a similar manner. Mutagenesis further showed that methionine residues in this pocket contribute to substrate binding and catalysis. Together, these results define the structural and sequence basis for PahB activity toward HMW-PAH-derived dihydrodiols and expand our understanding of the downstream catabolism of carcinogenic HMW-PAHs.IMPORTANCEHigh-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs) are persistent environmental contaminants with well-recognized carcinogenic risks. During aerobic catabolism, cis-dihydrodiol intermediates produced by ring-hydroxylating oxygenases must be oxidized by dihydrodiol dehydrogenases to enter the ring-cleavage pathway, making this second step essential for the overall degradation process. However, no structural information has been available for dehydrogenases capable of processing HMW-PAH intermediates. Previous work has focused mainly on the substrate range of ring-hydroxylating oxygenases, with much less attention to the substrate specificity of downstream dehydrogenases. Here, we elucidate the catalytic and structural basis by which PahB oxidizes dihydrodiols derived from four- and five-ring PAHs, including benzo[a]pyrene. We further show that M219-mediated conformational adaptability is a key structural feature that enables accommodation of bulky substrates beyond the traditional naphthalene- and biphenyl-based systems. These findings expand our understanding of the downstream determinants of HMW-PAH biodegradation and provide a structural basis for engineering dehydrogenases to improve microbial detoxification of carcinogenic PAHs in contaminated environments. PubMed: 42340355DOI: 10.1128/aem.00121-26 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.35 Å) |
Structure validation
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