A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 1, 2009, Pages 174-180

  Giardina, Giorgio ^a   Rinaldo, Serena ^a   Castiglione, Nicoletta ^a   Caruso, Manuela ^a   Cutruzzolà, Francesca ^a,b  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b NATIONAL INSTITUTE OF BIOSTRUCTURES AND BIOSYSTEMS   (Italy)

Author keywords

Denitrification; Heme sensor; Hemeprotein; Nitric oxide; Nitrite reductase; NO sensing; Transcription factor

Indexed keywords

DISSIMILATIVE NITRATE RESPIRATION REGULATOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DENITRIFYER; PRIORITY JOURNAL; PROTEIN STRUCTURE; PSEUDOMONAS AERUGINOSA; STRUCTURE ANALYSIS; WILD TYPE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; MOLECULAR SEQUENCE DATA; NITRITE REDUCTASES; OXIDOREDUCTASES; PROTEIN STRUCTURE, SECONDARY; PSEUDOMONAS AERUGINOSA; TRANSCRIPTION FACTORS;

PSEUDOMONAS AERUGINOSA;

EID: 70349334424     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22428     Document Type: Article

References (36)

1. Hakki M, Limaye AP, Kim HW, Kirby KA, Corey L, Boeckh M. Invasive Pseudomonas aeruginosa infections: high rate of recurrence and mortality after hematopoietic cell transplantation. Bone Marrow Transplant 2007;39:687-693. (Pubitemid 46813585)
2. Hassett DJ, Sutton MD, Schurr MJ, Herr AB, Caldwell CC, Matu JO. Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends Microbiol 2009;17:130-138
3. Alvarez-Ortega C, Harwood CS. Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration. Mol Microbiol 2007;65:153-165. (Pubitemid 46934486)
4. Yoon SS, Hennigan RF, Hilliard GM, Ochsner UA, Parvatiyar K, Kamani MC, Allen HL, DeKievit TR, Gardner PR, Schwab U, Rowe JJ, Iglewski BH, McDermott TR, Mason RP, Wozniak DJ, Hancock RE, Parsek MR, Noah TL, Boucher RC, Hassett DJ. Pseudomonas aeruginosa anaerobic respiration in biofilms: relationships to cystic fibrosis pathogenesis. Dev Cell 2002;3:593-603. (Pubitemid 35252267)
5. Hassett DJ, Cuppoletti J, Trapnell B, Lymar SV, Rowe JJ, Yoon SS, Hilliard GM, Parvatiyar K, Kamani MC, Wozniak DJ, Hwang SH, McDermott TR, Ochsner UA. Anaerobic metabolism and quorum sensing by Pseudomonas aeruginosa biofilms in chronically infected cystic fibrosis airways: rethinking antibiotic treatment strategies and drug targets. Adv Drug Deliv Rev 2002;54:1425-1443. (Pubitemid 35375769)
6. Spiro S. Regulators of bacterial responses to nitric oxide. FEMS Microbiol Rev 2007;31:193-211. (Pubitemid 46227144)
7. Barraud N, Hassett DJ, Hwang SH, Rice SA, Kjelleberg S, Webb JS. Involvement of nitric oxide in biofilm dispersal of Pseudomonas aeruginosa. J Bacteriol 2006;188:7344-7353. (Pubitemid 44646233)
8. Van Alst NE, Picardo KF, Iglewski BH, Haidaris CG. Nitrate sensing and metabolism modulate motility, biofilm formation, and virulence in Pseudomonas aeruginosa. Infect Immun 2007;75:3780-3790. (Pubitemid 47206275)
9. Arai H, Kodama T, Igarashi Y. Cascade regulation of the two CRP/FNR-related transcriptional regulators (ANR and DNR) and the denitrification enzymes in Pseudomonas aeruginosa. Mol Microbiol 1997;25:1141-1148. (Pubitemid 27410192)
10. Arai H, Igarashi Y, Kodama T. Expression of the nir and nor genes for denitrification of Pseudomonas aeruginosa requires a novel CRP/FNR-related transcriptional regulator. DNR, in addition to ANR. FEBS Lett 1995;371:73-76.
11. Korner H, Sofia HJ, Zumft WG. Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 2003;27:559-592. (Pubitemid 37456858)
12. Schultz SC, Shields GC, Steitz TA. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 1991;253:1001-1007.
13. Spiro S. The FNR family of transcriptional regulators. Antonie Van Leeuwenhoek 1994;66:23-36.
14. Yoon SS, Karabulut AC, Lipscomb JD, Hennigan RF, Lymar SV, Groce SL, Herr AB, Howell ML, Kiley PJ, Schurr MJ, Gaston B, Choi KH, Schweizer HP, Hassett DJ. Two-pronged survival strategy for the major cystic fibrosis pathogen. Pseudomonas aeruginosa, lacking the capacity to degrade nitric oxide during anaerobic respiration. EMBO J 2007;26:3662-3672.
15. Giardina G, Rinaldo S, Johnson KA, Di Matteo A, Brunori M, Cutruzzola F. NO sensing in Pseudomonas aeruginosa: structure of the transcriptional regulator DNR. J Mol Biol 2008;378:1002-1015.
16. Popov AN, Bourenkov GP. Choice of data-collection parameters based on statistic modelling. Acta Crystallogr D Biol Crystallogr 2003;59:1145-1153.
17. Leslie AGW. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EACBM newsletter on protein. Crystallography 1992;n.26.
18. Evans PR. Scala. Joint CCP4 and ESF-EACBM newsletter on protein. Crystallography 1997;3322-3324
19. McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ. Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr 2005;61:458-464.
20. CCP4 (Collaborative Computational Project N4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
21. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics 2006; Ch 5, Unit 5.6.
22. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60(Pt 12 Pt 1):2126-2132. (Pubitemid 41742764)
23. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997;53(Pt 3):240-255.
24. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins 1992;12:345-364.
25. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
26. Hodis E, Schreiber G, Rother K, Sussman JL. eMovie: a storyboard-based tool for making molecular movies. Trends Biochem Sci 2007;32:199-204. (Pubitemid 46694333)
27. Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH. Aromatic hydrogen bond in sequence-specific protein DNA recognition. Nat Struct Biol 1996;3:837-841. (Pubitemid 26330632)
28. Lanzilotta WN, Schuller DJ, Thorsteinsson MV, Kerby RL, Roberts GP, Poulos TL. Structure of the CO sensing transcription activator CooA. Nat Struct Biol 2000;7:876-880.
29. Eiting M, Hageluken G, Schubert WD, Heinz DW. The mutation G145S in PrfA, a key virulence regulator of Listeria monocytogenes, increases DNA-binding affinity by stabilizing the HTH motif. Mol Microbiol 2005;56:433-446. (Pubitemid 40516782)
30. Levy C, Pike K, Heyes DJ, Joyce MG, Gabor K, Smidt H, van der Oost J, Leys D. Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator. Mol Microbiol 2008;70:151-167.
31. Kim J, Adhya S, Garges S. Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation. Proc Natl Acad Sci USA 1992;89:9700-9704.
32. Yu S, Lee JC. Role of residue 138 in the interdomain hinge region in transmitting allosteric signals for DNA binding in Escherichia coli cAMP receptor protein. Biochemistry 2004;43:4662-4669. (Pubitemid 38509086)
33. Borjigin M, Li H, Lanz ND, Kerby RL, Roberts GP, Poulos TL. Structure-based hypothesis on the activation of the CO-sensing transcription factor CooA. Acta Crystallogr D Biol Crystallogr 2007;63(Pt 3):282-287. (Pubitemid 46438520)
34. Harman JG. Allosteric regulation of the cAMP receptor protein. Biochim Biophys Acta 2001;1547:1-17.
35. Kitanishi K, Igarashi J, Hayasaka K, Hikage N, Saiful I, Yamauchi S, Uchida T, Ishimori K, Shimizu T. Heme-binding characteristics of the isolated PAS-A domain of mouse Per2, a transcriptional regulatory factor associated with circadian rhythms. Biochemistry 2008;47:6157-6168. (Pubitemid 351812828)
36. Igarashi J, Murase M, Iizuka A, Pichierri F, Martinkova M, Shimizu T. Elucidation of the heme binding site of heme-regulated eukaryotic initiation factor 2alpha kinase and the role of the regulatory motif in heme sensing by spectroscopic and catalytic studies of mutant proteins. J Biol Chem 2008;283:18782-18791.