Structural variations in protein superfamilies: Actin and tubulin

Molecular Biotechnology

Volumn 42, Issue 1, 2009, Pages 49-60

  Wade, Richard H ^a   Garcia Saez, Isabel ^a   Kozielski, Frank ^b  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b BEATSON INSTITUTE FOR CANCER RESEARCH   (United Kingdom)

Author keywords

Actin; Structure variation in protein families; Tubulin

Indexed keywords

ACTIN; ACTIVE SITE RESIDUES; AMINO ACID RESIDUES; CORE STRUCTURE; CYTOSKELETONS; HOMOLOGOUS PROTEINS; PROTEIN FAMILY; STRUCTURAL VARIATIONS; STRUCTURE VARIATION IN PROTEIN FAMILIES; SURFACE LOOPS; TUBULIN;

AMINES; AMINO ACIDS; ORGANIC ACIDS; PROTEINS;

CYTOTOXICITY;

ACTIN; ACTIN RELATED PROTEIN; ALPHA TUBULIN; BETA TUBULIN; CYTOSKELETON PROTEIN; GAMMA TUBULIN; MREB PROTEIN; TUBULIN; ACTIN BINDING PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; NONHUMAN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE; STRUCTURAL PROTEOMICS; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; INDEL MUTATION; INTRON; PROTEIN DATABASE;

EUKARYOTA; METAZOA;

ACTINS; AMINO ACID MOTIFS; ANIMALS; DATABASES, PROTEIN; HUMANS; INDEL MUTATION; INTRONS; MICROFILAMENT PROTEINS; MODELS, MOLECULAR; TUBULIN;

EID: 69149095478     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-008-9128-6     Document Type: Article

References (46)

1. I Jonassen JF Collins PG Higgins 1995 Finding flexible patterns in unaligned protein sequences Protein Science 4 1587 1595 10.1002/pro.5560040817 1:CAS:528:DyaK2MXnvVyjsL0%3D
2. K Ye WA Kosters A Ijerman 2007 An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences Bioinformatics 23 687 693 10.1093/bioinformatics/btl665 1:CAS:528: DC%2BD2sXkt1Ght7w%3D (Pubitemid 46554719)
3. RH Wade 2002 Sequence landmark patterns identify and characterize protein families Structure 10 1329 1336 10.1016/S0969-2126(02)00854-7 1:CAS:528:DC%2BD38XnvVOrtbc%3D (Pubitemid 35232382)
4. MJTV Cope J Whisstock I Rayment J Kendrick-Jones 1996 Conservation within the myosin motor domain: Implications for structure and function Structure 4 969 987 10.1016/S0969-2126(96)00103-7 1:CAS:528:DyaK28Xlt1SjtL4%3D (Pubitemid 26324708)
5. AJ Kim SA Endow 2000 A kinesin family tree Journal of Cell Science 113 3681 3682 1:CAS:528:DC%2BD3cXosVGmtL4%3D
6. JM McDowell S Huang EC McKinney YQ An RB Meagher 1996 Structure and evolution of the actin gene family in Arabidopsis thaliana Genetics 142 587 602 1:CAS:528:DyaK28XhsFKjs7g%3D (Pubitemid 26039227)
7. MK Kandasamy EC McKinney RB Meagher 2002 Functional nonequivalency of actin isovariants in Arabidopsis Molecular Biology of the Cell 13 251 261 10.1091/mbc.01-07-0342 1:CAS:528:DC%2BD38XnvFCitQ%3D%3D (Pubitemid 34106073)
8. CA Blessing GT Ugrinova HV Goodson 2004 Actin and Arps: Action in the nucleus Trends in Cell Biology 14 435 442 10.1016/j.tcb.2004.07.009 1:CAS:528:DC%2BD2cXmsl2isbc%3D (Pubitemid 39092701)
9. O Poch B Winsor 1997 Who's who among the Saccharomyces cerivisiae actin-related proteins? A classification and nomenclature proposal for a large family Yeast 13 1053 1058 10.1002/(SICI)1097-0061(19970915)13:11<1053::AID- YEA164>3.0.CO;2-4 1:CAS:528:DyaK2sXls1GqurY%3D (Pubitemid 27368515)
10. HV Goodson WF Hawse 2002 Molecular evolution of the actin family Journal of Cell Science 115 2619 2622 1:CAS:528:DC%2BD38XlsFCrt7o%3D
11. H Szerlong A Saha BR Cairns 2003 The nuclear actin-related proteins Arp7 and Arp9: A dimeric module that cooperates with architectural proteins for chromatin remodeling EMBO Journal 22 3175 3187 10.1093/emboj/cdg296 1:CAS:528:DC%2BD3sXks1Wqsr4%3D (Pubitemid 36758637)
12. W Kabsch HG Mannherz D Suck EF Pai KC Holmes 1990 Atomic structure of the actin:DNase 1 complex Nature 347 37 44 10.1038/347037a0 1:CAS:528: DyaK3cXls1yjsLk%3D (Pubitemid 20280179)
13. LR Otterbein P Graceffa R Dominguez 2001 The crystal structure of uncomplexed actin in the ADP state Science 293 708 711 10.1126/science.1059700 1:CAS:528:DC%2BD3MXls1Kmt7Y%3D
14. S Vorobiev B Strokopytov DG Drubin C Frieden S Ono J Condeelis PA Rubenstein SC Almo 2003 The structure of nonvertebrate actin: Implications for the ATP hydrolytic mechanism Proceedings of the National Academy of Sciences of the United States of America 100 5760 5765 10.1073/pnas.0832273100 1:CAS:528:DC%2BD3sXjvFOls7o%3D (Pubitemid 36576881)
15. RC Robinson K Turbedsky DA Kaiser J-B Marchand HN Higgs S Choe TD Pollard 2001 Crystal structure of Arp2/3 complex Science 294 1679 1684 10.1126/science.1066333 1:CAS:528:DC%2BD3MXoslequ7w%3D (Pubitemid 33104831)
16. BJ Nolen RS Littlefield TD Pollard 2004 Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP Proceedings of the National Academy of Sciences of the United States of America 101 15627 15632 10.1073/pnas.0407149101 1:CAS:528:DC%2BD2cXhtVWisLvM (Pubitemid 39473538)
17. F van den Ent LA Amos J Löwe 2001 Prokaryotic origin of the actin cytoskeleton Nature 413 39 44 10.1038/35092500 (Pubitemid 32843480)
18. F van den Ent J Löwe 2000 Crystal structure of the cell division protein FtsA EMBO Journal 19 5300 5307 10.1093/emboj/19.20.5300
19. F van den Ent J Moller-Jensen LA Amos K Gerdes J Löwe 2002 F-actin-like filaments formed by plasmid segregation protein ParM EMBO Journal 21 6935 6943 10.1093/emboj/cdf672 (Pubitemid 36014565)
20. KW Wood WD Cornwell JR Jackson 2001 Past and future of the mitotic spindle as an oncology target Current Opinion in Pharmacology 1 370 377 10.1016/S1471-4892(01)00064-9 1:CAS:528:DC%2BD3MXlsVelsrk%3D (Pubitemid 33585986)
21. RF Ludueña 1998 Multiple forms of tubulin: Different gene products and covalent modifications International Review of Cytology 178 207 275 10.1016/S0074-7696(08)62138-5
22. CE Oakley BR Oakley 1989 Identification of γ-tubulin, a new member of the tubulin superfamily encoded by mipA gene of Aspergillus nidulans Nature 338 662 664 10.1038/338662a0 1:CAS:528:DyaL1MXlsVOksr8%3D (Pubitemid 19104647)
23. BR Oakley 1992 γ-tubulin: The microtubule organiser? Trends in Cell Biology 2 1 5 10.1016/0962-8924(92)90125-7 1:CAS:528:DyaK3sXktVeisbs%3D
24. SK Dutcher 2003 Long-lost relatives reappear: Identification of new members of the tubulin superfamily Current Opinion in Microbiology 6 634 640 10.1016/j.mib.2003.10.016 1:CAS:528:DC%2BD3sXps1yjs70%3D (Pubitemid 38020062)
25. JB Dictenberg W Zimmerman CA Sparks A Young C Vidair Y Zheng W Carrington FS Fay SJ Doxsey 1998 Pericentrin and γ-tubulin form a protein complex and are organised into a novel lattice at the centrosome Journal of Cell Biology 141 163 174 10.1083/jcb.141.1.163 1:CAS:528:DyaK1cXis1ejs78%3D (Pubitemid 28182649)
26. PG McKean S Vaughan K Gull 2001 The extended tubulin superfamily Journal of Cell Science 114 2723 2733 1:CAS:528:DC%2BD3MXmt1Wgu74%3D
27. NW Goehring J Beckwith 2005 Diverse paths to midcell: Assembly of the bacterial cell division machinery Current Biology 15 R514 R526 10.1016/j.cub.2005.06.038 1:CAS:528:DC%2BD2MXlvFygtrc%3D (Pubitemid 40950512)
28. HP Erickson 1997 FtsZ, a tubulin homologue in prokaryote cell division Trends in Cell Biology 7 362 370 10.1016/S0962-8924(97)01108-2 1:CAS:528:DyaK2sXlvFels7k%3D (Pubitemid 27384782)
29. J Löwe LA Amos 1998 Crystal structure of the bacterial cell division protein FtsZ Nature 391 203 206 10.1038/34472 (Pubitemid 28092483)
30. E Nogales KH Downing LA Amos J Löwe 1998 Tubulin and FtsZ form a distinct family of GTPases Nature Structural Biology 5 451 458 10.1038/nsb0698-451 1:CAS:528:DyaK1cXjslCktLY%3D (Pubitemid 28265028)
31. MA Oliva SC Cordell J Löwe 2004 Structural insights into FtsZ protofilament formation Nature Structural & Molecular Biology 11 1243 1250 10.1038/nsmb855 1:CAS:528:DC%2BD2cXhtVens7vL
32. H Aldaz LM Rice T Stearns DA Agard 2005 Insights into microtubule nucleation from the crystal structure of human γ-tubulin Nature 435 523 527 10.1038/nature03586 1:CAS:528:DC%2BD2MXksVeis7w%3D (Pubitemid 40734251)
33. DeLano, W. L. (2002). The PyMol molecular graphics system. San Carlos, CA: DeLano Scientific.
34. J Löwe H Li KH Downing E Nogales 2001 Refined structure of αβ-tubulin at 3.5 Å resolution Journal of Molecular Biology 313 1045 1057 10.1006/jmbi.2001.5077 (Pubitemid 33081900)
35. C Combet C Blanchet C Geourjon G Deléage 2000 NPS@: Network protein sequence analysis Trends in Biological Sciences 25 147 150 10.1016/S0968-0004(99)01540-6 1:CAS:528:DC%2BD3cXhsleiu7Y%3D (Pubitemid 30122428)
36. ET Steenkamp J Wright SL Baldauf 2006 The protistan origins of animals and fungi Molecular Biology and Evolution 23 93 106 10.1093/molbev/msj011 1:CAS:528:DC%2BD2MXhtleqtLjP (Pubitemid 41785957)
37. E Nogales SG Wolf KH Downing 1998 Structure of the αβ-tubulin dimer by electron crystallography Nature 391 199 203 10.1038/34465 1:CAS:528:DyaK1cXmt1Kisw%3D%3D (Pubitemid 28092482)
38. YF Inclan E Nogales 2001 Structural models for the self assembly and microtubule interactions of γ-, δ- and ε-tubulin Journal of Cell Science 114 413 422 1:CAS:528:DC%2BD3MXht1KgurY%3D
39. P Bork C Sander A Valencia 1992 An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins Proceedings of the National Academy of Sciences of the United States of America 89 7290 7294 10.1073/pnas.89.16.7290 1:CAS:528:DyaK3sXlsFSjtw%3D%3D
40. KE Croft AB Dalby DJ Hogan KE Orr EA Hewitt RJ Africa ML DuBois DM Prescott 2003 Macronuclear molecules encoding actins in spirotrichs Journal of Molecular Evolution 56 341 350 10.1007/s00239-002-2405-2 1:CAS:528: DC%2BD3sXhslWhsrs%3D (Pubitemid 36279038)
41. L Holm J Park 2000 DaliLite workbench for protein structure comparison Bioinformatics 16 566 567 10.1093/bioinformatics/16.6.566 1:CAS:528: DC%2BD3cXnsVeltr8%3D
42. CC Beltzner TD Pollard 2004 Identification of functionally important residues of the Arp2/3 complex by analysis of homology models from diverse species Journal of Molecular Biology 336 551 565 10.1016/j.jmb.2003.12.017 1:CAS:528:DC%2BD2cXntVKqsw%3D%3D (Pubitemid 38147646)
43. J Muller Y Oma L Vallar E Friederich O Poch B Winsor 2005 Sequence and comparative genomic analysis of actin-related proteins Molecular Biology of the Cell 16 5736 5748 10.1091/mbc.E05-06-0508 1:CAS:528:DC%2BD2MXht12gsLbK (Pubitemid 41752222)
44. L Carmel IB Rogozin YI Wolf EV Koonin 2007 Evolutionarily conserved genes preferentially accumulate introns Genome Research 17 1045 1050 10.1101/gr.5978207 1:CAS:528:DC%2BD2sXnvVWkuro%3D (Pubitemid 47026351)
45. T Sadunsky AJ Newmann NJ Dibb 2004 Exon junction sequences as cryptic splice sites: Implications for intron origin Current Biology 14 505 509
46. CS Craik RJ Rutter R Fletterick 1983 Splice junctions: Association with variation in protein structure Science 220 1125 1129 10.1126/science.6344214 1:CAS:528:DyaL3sXks1Ght7w%3D