Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: A structural model of its N-terminal domain

Environmental Microbiology

Volumn 4, Issue 1, 2002, Pages 29-41

  Devos, D ^a   Garmendia, J ^a   De Lorenzo, V ^a   Valencia, A ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); PROKARYOTA; PSEUDOMONAS;

3 XYLENE; 3-XYLENE; BACTERIAL PROTEIN; DMPR PROTEIN, PSEUDOMONAS; DNA BINDING PROTEIN; TOLUENE; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR; XYLENE; XYLR PROTEIN, PSEUDOMONAS;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; METABOLISM; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; PSEUDOMONAS; RAT; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PSEUDOMONAS; RATS; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP; TOLUENE; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; XYLENES;

EID: 0036009684     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2002.00265.x     Document Type: Article

References (49)

1. Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway
2. Basic local alignment search tool
3. The black cat/white cat principle of signal integration in bacterial promoters
4. Jpred: A consensus secondary structure prediction server
5. Genetic evidence for activation of the positive transcriptional regulator XylR, a member of the NtrC family of regulators, by effector binding
6. Single amino acids changes in the signal receptor domain of XylR resulted in mutants that stimulate transcription in the absence of effectors
7. Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains
8. The role of the interdomain B linker in the activation of the XylR protein of Pseudomonas putida
9. A la carte transcriptional regulators: Unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors
10. Errors in protein structures
11. HbpR, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1
12. Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure
13. Structure of a transiently phosphorylated switch in bacterial signal transduction
14. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
15. 54 (ntrA)-dependent genes is probably united by a common mechanism
16. A simple method for displaying the hydropathic character of a protein
17. PROCHECK: A program to check the stereochemical quality of protein structures
18. Crystal structure of activated CheY
19. Crystal structure of an activated response regulator bound to its target
20. Analysis and construction of stable phenotypes in Gram-negative bacteria with Tn5- and Tn10-derived minitransposons
21. 54-dependent activator DmpR
22. Protein folding and association, insight from the interfacial and thermodynamic properties of hydrocarbons
23. Prokaryotic enhancer-binding proteins reflect eukaryote-like modularity: Puzzle of nitrogen regulatory protein C
24. Effective use of sequence correlation and conservation in fold recognition
25. 54-dependent regulator DmpR
26. CATH - A hierarchic classification of protein domain structures
27. An aromatic effector specificity mutant of the transcriptional regulator DmpR overcomes the growth constraints of Pseudomonas sp. strain CF600 on para-substituted methylphenols
28. Correlated mutations contain information about protein-protein interaction
29. Comparative analysis of different methods for the detection of specificity regions in protein families
30. A platform for integrating threading results with protein family analyses
31. The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor
32. Identification of the repressor subdomain within the signal reception module of the prokaryotic enhancer-binding protein XylR of Pseudomonas putida
33. In vitro activities of an N-terminal truncated form of XylRm a sigma 54-dependent transcriptional activator of Pseudomonas putida
34. ATP binding to the sigma 54-dependent activator XylR triggers a protein multimerization cycle catalysed by UAS DNA
35. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators
36. PHD: Predicting one-dimensional protein structure by profile based neural networks
37. Twilight zone of protein sequence alignments
38. Comparative protein modelling by satisfaction of spatial restraints
39. Modulation of the function of the signal receptor domains of XylR, a member of a family of prokaryotic enhancer-like positive regulators
40. Database of homology derived protein structures and the structural meaning of sequence alignment
41. Role of the DmpR-mediated regulatory circuit in bacterial biodegradation properties in methylphenol-amended soils
42. 54-dependent regulators: Derepression as a control mechanism
43. Direct regulation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds
44. Recognition of errors in three-dimensional structures of proteins
45. Identification of an effector specificity subregion within the aromatic responsive regulators DmpR and XylR by DNA shuffling
46. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
47. Crystal structure of catechol O-methyltransferase
48. The Q-linker: A class of interdomain sequences found in bacterial multidomain regulatory proteins
49. The molecular structure of wild-type and a mutant Fis protein: Relationship between mutational changes and recombinational enhancer function or DNA binding