TPR domain of NrfG mediates complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia coli O157:H7

Proteins: Structure, Function and Genetics

Volumn 70, Issue 3, 2008, Pages 900-914

  Han, Dohyun ^a   Kim, Kyunggon ^a   Oh, Jongkil ^a   Park, Jungeun ^a   Kim, Youngsoo ^a  

^a Seoul National University   (South Korea)

Author keywords

Cytochrome C; E. coli O157; Formate dependent nitrite reductase; Heme lyase; NrfA; NrfG; TPR

Indexed keywords

BACTERIAL PROTEIN; CYTOCHROME C; HEME LYASE; LYASE; NITRITE REDUCTASE; PROTEIN NRFG; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; COMPLEX FORMATION; CRYSTAL STRUCTURE; ESCHERICHIA COLI O157; NITRATE METABOLISM; NONHUMAN; NRFE GENE; NRFF GENE; NRFG GENE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; CYTOCHROME C GROUP; ESCHERICHIA COLI O157; ESCHERICHIA COLI PROTEINS; GENES, BACTERIAL; LYASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NITRITE REDUCTASES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

ESCHERICHIA COLI;

EID: 38549150882     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21597     Document Type: Article

References (46)

1. Perna NT, Plunkett G, III, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001;409:529-533.
2. Iobbi-Nivol C, Crooke H, Griffiths L, Grove J, Hussain H, Pommier J, Mejean V, Cole JA. A reassessment of the range of c-type cytochromes synthesized by Escherichia coli K-12. FEMS Microbiol Lett 1994;119:89-94.
3. Fujita T. Studies on soluble cytochromes in Enterobacteriaceae. I. Detection, purification, and properties of cytochrome c-552 in anaerobically grown cells. J Biochem 1966;60:204-215.
4. Fujita T. Studies on soluble cytochromes in Enterobacteriaceae. II. Cytochromes b-562 and c-550. J Biochem 1966;60:329-334.
5. Grove J, Tanapongpipat S, Thomas G, Griffiths L, Crooke H, Cole J. Escherichia coli K-12 genes essential for the synthesis of c-type cytochromes and a third nitrate reductase located in the periplasm. Mol Microbiol 1996;19:467-481.
6. Eaves DJ, Grove J, Staudenmann W, James P, Poole RK, White SA, Griffiths I, Cole JA. Involvement of products of the nrfEFG genes in the covalent attachment of haem c to a novel cysteine-lysine motif in the cytochrome c552 nitrite reductase from Escherichia coli. Mol Microbiol 1998;28:205-216.
7. Berks BC, Ferguson SJ, Moir JW, Richardson DJ. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim Biophys Acta 1995;1232:97-173.
8. Kranz R, Lill R, Goldman B, Bonnard G, Merchant S. Molecular mechanisms of cytochrome c biogenesis: three distinct systems. Mol Microbiol 1998;29:383-396.
9. Thony-Meyer L. Cytochrome c maturation: a complex pathway for a simple task? Biochem Soc Trans 2002;30:633-638.
10. Thony-Meyer L, Fischer F, Kunzler P, Ritz D, Hennecke H. Escherichia coli genes required for cytochrome c maturation. J Bacteriol 1995;177:4321-4326.
11. Hussain H, Grove J, Griffiths L, Busby S, Cole J. A seven-gene operon essential for formate-dependent nitrite reduction to ammonia by enteric bacteria. Mol Microbiol 1994;12:153-163.
12. Grove J, Busby S, Cole J. The role of the genes nrf EFG and ccmFH in cytochrome c biosynthesis in Escherichia coli. Mol Gen Genet 1996;252:332-341.
13. Ren Q, Ahuja U, Thony-Meyer L. A bacterial cytochrome c heme lyase. CcmF forms a complex with the heme chaperone CcmE and CcmH but not with apocytochrome c. J Biol Chem 2002;277:7657-7663.
14. D'Andrea LD, Regan L. TPR proteins: the versatile helix. Trends Biochem Sci 2003;28:655-662.
15. Wilson CG, Kajander T, Regan L. The crystal structure of NlpI. A prokaryotic tetratricopeptide repeat protein with a globular fold. FEBS J 2005;272:166-179.
16. Sikorski RS, Boguski MS, Goebl M, Hieter P. A repeating amino acid motif in CDC23 defines a family of proteins and a new relationship among genes required for mitosis and RNA synthesis. Cell 1990;60:307-317.
17. Das AK, Cohen PW, Barford D. The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J 1998;17:1192-1199.
18. Magliery TJ, Regan L. Beyond consensus: statistical free energies reveal hidden interactions in the design of a TPR motif. J Mol Biol 2004;343:731-745.
19. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
20. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr 1999;55:849-861.
21. Terwilliger TC. Maximum-likelihood density modification. Acta Crystallogr 2000;56:965-972.
22. Terwilliger TC. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr 2003; 59:38-44.
23. Terwilliger T. Solve and resolve: automated structure solution, density modification and model building. J Synchrotron Radiat 2004; 11:49-52.
24. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47 (Part 2): 110-119.
25. Kleywegt GJ, Jones TA. xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr 1996;52:826-828.
26. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr 2004;60:2126-2132.
27. Winn MD, Isupov MN, Murshudov GN. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr 2001;57:122-133.
28. Winn MD, Ashton AW, Briggs PJ, Ballard CC, Patel P. Ongoing developments in CCP4 for high-throughput structure determination. Acta Crystallogr 2002;58:1929-1936.
29. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
30. Hutchinson EG, Thornton JM. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci 1996;5:212-220.
31. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
32. Kim K, Oh J, Han D, Kim EE, Lee B, Kim Y. Crystal structure of PilF: functional implication in the type 4 pilus biogenesis in Pseudomonas aeruginosa. Biochem Biophys Res Commun 2006;340: 1028-1038.
33. Main ER, Stott K, Jackson SE, Regan L. Local and long-range stability in tandemly arrayed tetratricopeptide repeats. Proc Natl Acad Sci USA 2005;102:5721-5726.
34. Main ER, Xiong Y, Cocco MJ, D'Andrea L, Regan L. Design of stable α-helical arrays from an idealized TPR motif. Structure 2003;11:497-508.
35. Jinek M, Rehwinkel J, Lazarus BD, Izaurralde E, Hanover JA, Conti E. The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin α. Nat Struct Mol Biol 2004;11:1001-1007.
36. Gatto GJ, Jr, Geisbrecht BV, Gould SJ, Berg JM. Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nat Struct Biol 2000;7:1091-1095.
37. Kumar A, Roach C, Hirsh IS, Turley S, deWalque S, Michels PA, Hol WG. An unexpected extended conformation for the third TPR motif of the peroxin PEX5 from Trypanosoma brucei. J Mol Biol 2001;307:271-282.
38. Bamford VA, Angove HC, Seward HE, Thomson AJ, Cole JA, Butt JN, Hemmings AM, Richardson DJ. Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli. Biochemistry 2002;41:2921-2931.
39. Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, Kroneck PM. Structure of cytochrome c nitrite reductase. Nature 1999;400:476-480.
40. Einsle O, Stach P, Messerschmidt A, Simon J, Kroger A, Huber R, Kroneck PM. Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and hemepacking motifs. J Biol Chem 2000;275:39608-39616.
41. Scheufler C, Brinker A, Bourenkov G, Pegoraro S, Moroder L, Bartunik H, Hartl FU, Moarefi I. Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine. Cell 2000;101:199-210.
42. Zhang M, Windheim M, Roe SM, Peggie M, Cohen P, Prodromou C, Pearl LH. Chaperoned ubiquitylation - crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex. Mol Cell 2005;20:525-538.
43. Karpenahalli MR, Lupas AN, Soding J. TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinformatics 2007;8:2.
44. Pisa R, Stein T, Eichler R, Gross R, Simon J. The nrfI gene is essential for the attachment of the active site haem group of Wolinella succinogenes cytochrome c nitrite reductase. Mol Microbiol 2002;43: 763-770.
45. Cinege G, Kereszt A, Kertesz S, Balogh G, Dusha I. The roles of different regions of the CycH protein in c-type cytochrome biogenesis in Sinorhizobium meliloti. Mol Genet Genomics 2004;271:171-179.
46. Fabianek RA, Hofer T, Thony-Meyer L. Characterization of the Escherichia coli CcmH protein reveals new insights into the redox pathway required for cytochrome c maturation. Arch Microbiol 1999;171:92-100.