9ISW
Crystal structure of AlkR (VanR), a GntR family transcriptional regulator
Summary for 9ISW
| Entry DOI | 10.2210/pdb9isw/pdb |
| Descriptor | Transcriptional regulator (2 entities in total) |
| Functional Keywords | a gntr family transcriptional regulator, dna binding protein |
| Biological source | Pseudomonas aeruginosa |
| Total number of polymer chains | 1 |
| Total formula weight | 25102.89 |
| Authors | |
| Primary citation | Peng, W.,Wang, X.,Liu, Q.,Xiao, Z.,Li, F.,Ji, N.,Chen, Z.,He, J.,Wang, J.,Deng, Z.,Lin, S.,Liang, R. The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n -alkane degradation in Pseudomonas aeruginosa SJTD-1. Mlife, 4:126-142, 2025 Cited by PubMed Abstract: Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain -alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of enhanced the transcription levels of the gene and the utilization efficiency of the medium-to-long-chain -alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the 2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of 2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for -alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating -alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution. PubMed: 40313978DOI: 10.1002/mlf2.70004 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.86 Å) |
Structure validation
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