The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu

Protein Science

Volumn 19, Issue 11, 2010, Pages 2131-2140

  Das, Debanu ^a,b   Finn, Robert D ^c   Abdubek, Polat ^a,d   Astakhova, Tamara ^a,e   Axelrod, Herbert L ^a,b   Bakolitsa, Constantina ^a,f   Cai, Xiaohui ^a,e   Carlton, Dennis ^a,g   Chen, Connie ^a,d   Chiu, Hsiu Ju ^a,b   Chiu, Michelle ^a,d   Clayton, Thomas ^a,g   Deller, Marc C ^a,g   Duan, Lian ^a,e   Ellrott, Kyle ^a,f   Farr, Carol L ^a,g   Feuerhelm, Julie ^a,d   Grant, Joanna C ^a,d   Grzechnik, Anna ^a,g   Han, Gye Won ^a,g   Jaroszewski, Lukasz ^a,e,f   Jin, Kevin K ^a,b   Klock, Heath E ^a,d   Knuth, Mark W ^a,d   Kozbial, Piotr ^a,f   Sri Krishna, S ^a,e,f   Kumar, Abhinav ^a,b   Lam, Winnie W ^a,b   Marciano, David ^a,g   Miller, Mitchell D ^a,b   Morse, Andrew T ^a,e   Nigoghossian, Edward ^a,d   Nopakun, Amanda ^a,g   Okach, Linda ^a,d   Puckett, Christina ^a,d   Reyes, Ron ^a,b   Tien, Henry J ^a,g   Trame, Christine B ^a,b   Van Den Bedem, Henry ^a,b   Weekes, Dana ^a,f   Wooten, Tiffany ^a,e   Xu, Qingping ^a,b   Yeh, Andrew ^a,b   Zhou, Jiadong ^a,d   Hodgson, Keith O ^a,h   Wooley, John ^a,e   Elsliger, Marc André ^a,g   Deacon, Ashley M ^a,b   Godzik, Adam ^a,e,f   Lesley, Scott A ^a,d,g   Wilson, Ian A ^a,g   more..

^a Joint Center for Structural Genomics   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f BURNHAM INSTITUTE   (United States)

^g SCRIPPS RESEARCH INSTITUTE   (United States)

^h SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

Neisseria gonorrhoeae; NGO1391; Pfam PF05076; Structural genomics; Sufu like; Suppressor of fused; UniProt Q5F6Z8

Indexed keywords

BACTERIAL PROTEIN; PROTEIN SUFU; SONIC HEDGEHOG PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; NEISSERIA GONORRHOEAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; NEISSERIA GONORRHOEAE; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; STATIC ELECTRICITY; STRUCTURAL HOMOLOGY, PROTEIN;

BACTERIA (MICROORGANISMS); ERINACEIDAE; EUKARYOTA; NEISSERIA GONORRHOEAE;

EID: 78349279938     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.497     Document Type: Article

References (50)

1. McMahon AP, Ingham PW, Tabin CJ (2003) Developmental roles and clinical significance of hedgehog signaling. Curr Top Dev Biol 53:1-114. (Pubitemid 137639458)
2. Jiang J, Hui CC (2008) Hedgehog signaling in development and cancer. Dev Cell 15:801-812.
3. Varjosalo M, Taipale J (2008) Hedgehog: functions and mechanisms. Genes Dev 22:2454-2472.
4. MacDonald BT, Tamai K, He X (2009) Wnt/beta-catenin signaling: components, mechanisms, and diseases. Dev Cell 17:9-26.
5. Pasca di Magliano M, Hebrok M (2003) Hedgehog signalling in cancer formation and maintenance. Nat Rev Cancer 3:903-911.
6. Lai SL, Chien AJ, Moon RT (2009) Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis. Cell Res 19:532-545.
7. Burglin TR (2008) The Hedgehog protein family. Genome Biol 9:241.
8. Burglin TR (2008) Evolution of hedgehog and hedge-hog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif. BMC Genomics 9:127.
9. Hausmann G, von Mering C, Basler K (2009) The hedgehog signaling pathway: where did it come from? PLoS Biol 7:e1000146.
10. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A (2008) The Pfam protein families database. Nucleic Acids Res 36:D281-D288.
11. Dunaeva M, Michelson P, Kogerman P, Toftgard R (2003) Characterization of the physical interaction of Gli proteins with SUFU proteins. J Biol Chem 278:5116-5122. (Pubitemid 36801022)
12. Merchant M, Vajdos FF, Ultsch M, Maun HR, Wendt U, Cannon J, Desmarais W, Lazarus RA, de Vos AM, de Sauvage FJ (2004) Suppressor of fused regulates Gli activity through a dual binding mechanism. Mol Cell Biol 24:8627-8641. (Pubitemid 39245082)
13. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 33:W284-W288. (Pubitemid 44529927)
14. Cruickshank DW (1999) Remarks about protein structure precision. Acta Crystallogr D Biol Crystallogr 55:583-601.
15. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491-497.
16. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
17. Holm L, Kaariainen S, Rosenstrom P, Schenkel A (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics 24:2780-2781.
18. Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19(Suppl 2):246-255. (Pubitemid 41296662)
19. Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256-2268. (Pubitemid 41742778)
20. Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2: Unit 2.3.
21. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33:W299-W302. (Pubitemid 44529930)
22. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C (2009) STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37:D412-D416.
23. Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D, Chillingworth T, Davies RM, Davis P, Devlin K, Feltwell T, Hamlin N, Holroyd S, Jagels K, Leather S, Moule S, Mungall K, Quail MA, Rajandream MA, Rutherford KM, Simmonds M, Skelton J, Whitehead S, Spratt BG, Barrell BG (2000) Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404:502-506.
24. Bentley SD, Vernikos GS, Snyder LA, Churcher C, Arrowsmith C, Chillingworth T, Cronin A, Davis PH, Holroyd NE, Jagels K, Maddison M, Moule S, Rabbinowitsch E, Sharp S, Unwin L, Whitehead S, Quail MA, Achtman M, Barrell B, Saunders NJ, Parkhill J (2007) Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. PLoS Genet 3:e23.
25. Krishna SS, Weekes D, Bakolitsa C, Elsliger MA, Wilson IA, Godzik A, Wooley J (2010) TOPSAN: Use of a Collaborative Environment for Annotating, Analyzing and Disseminating Data on JCSG and PSI structures. Acta Crystallogr F Struct Biol Cryst Commun 66:1143-1147.
26. Weekes D, Krishna SS, Bakolitsa C, Wilson IA, Godzik A, Wooley J (2010) TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinf 11:426.
27. Klock HE, Koesema EJ, Knuth MW, Lesley SA (2008) Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins 71:982-994.
28. Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol 229:105-124.
29. Santarsiero BD, Yegian DT, Lee CC, Spraggon G, Gu J, Scheibe D, Uber DC, Cornell EW, Nordmeyer RA, Kolbe WF, Jin J, Jones AL, Jaklevic JM, Schultz PG, Stevens RC (2002) An approach to rapid protein crystallization using nanodroplets. J Appl Crystallogr 35:278-281.
30. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC (2002) Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 99:11664-11669.
31. Cohen AE, Ellis PJ, Miller MD, Deacon AM, Phizackerley RP (2002) An automated system to mount cryocooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot. J Appl Crystallogr 2002:720-726.
32. McPhillips TM, McPhillips SE, Chiu HJ, Cohen AE, Deacon AM, Ellis PJ, Garman E, Gonzalez A, Sauter NK, Phizackerley RP, Soltis SM, Kuhn P (2002) Blu-ice and the distributed control system: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat 9:401-406.
33. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallog 26:795-800.
34. Collaborative Computing Project N(1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760-763.
35. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112-122.
36. Vonrhein C, Blanc E, Roversi P, Bricogne G (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364:215-230.
37. Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171-1179.
38. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486-501.
39. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximumlikelihood method. Acta Crystallogr D Biol Crystallogr 53:240-255.
40. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 60:1833-1839.
41. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52-56, 29.
42. Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 55:191-205.
43. Terwilliger TC (2000) Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 56:965-972.
44. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
45. Kleywegt GJ (2000) Validation of protein crystal structures. Acta Crystallogr D Biol Crystallogr 56:249-265.
46. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774-797.
47. Laskowski RA, Chistyakov VV, Thornton JM (2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33:D266-D268.
48. DeLano WL (2008) The PyMOL molecular graphics system. DeLano Scientific LLC: Palo Alto, CA, USA.
49. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35:W522-W525.
50. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041.