Domain atrophy creates rare cases of functional partial protein domains

Genome Biology

Volumn 16, Issue 1, 2015, Pages

  Prakash, Ananth ^a   Bateman, Alex ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE TRIPHOSPHATASE ACTIVATING PROTEIN; BACTERIAL PROTEIN; CARRIER PROTEIN; LUCIFERASE; LUXG PROTEIN, BACTERIA; OXIDOREDUCTASE;

2 HYDROXYACID DEHYDROGENASE NAD BINDING DOMAIN; ADENOSINE MONOPHOSPHATE BINDING DOMAIN; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; ARTIFACT; ATROPHY SCORE; BACTERIAL LUCIFERASE DOMAIN; BETA BARREL; C TERMINAL END BOUNDED ATROPHY; DOMAIN ATROPHY; DOWNSTREAM DOMAIN BOUNDED ATROPHY; FALSE POSITIVE RESULT; FUNCTIONAL PARTIAL PROTEIN DOMAIN; GLYCOSYL HYDROLASE FAMILY 10 DOMAIN; HUMAN; MOLECULAR MODEL; N TERMINAL END BOUNDED ATROPHY; NONBIOLOGICAL MODEL; NONHUMAN; PHOTOBACTERIUM PHOSPHOREUM; PHYLOGENETIC TREE; PROFILE HMM MODEL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; RAL GTPASE ACTIVATING PROTEIN DOMAIN; RNASE E G DOMAIN; ROSSMANN FOLD; SCORING SYSTEM; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; THREE DIMENSIONAL PROTEIN STRUCTURE; TIM BARREL FOLD; UPSTREAM DOMAIN BOUNDED ATROPHY; WITHIN DOMAIN ATROPHY; BACTERIAL GENE; BURKHOLDERIA CENOCEPACIA; ENZYMOLOGY; ESCHERICHIA COLI; FILOBASIDIELLA; GENE DELETION; GENETICS; LACTOBACILLUS; METABOLISM; MOLECULAR EVOLUTION; PHOTOBACTERIUM; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; PYROCOCCUS FURIOSUS; STAPHYLOCOCCUS AUREUS;

BACTERIAL PROTEINS; BURKHOLDERIA CENOCEPACIA; CARRIER PROTEINS; CRYPTOCOCCUS; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENE DELETION; GENES, BACTERIAL; HUMANS; LACTOBACILLUS; LUCIFERASES; MODELS, MOLECULAR; OXIDOREDUCTASES; PHOTOBACTERIUM; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PYROCOCCUS FURIOSUS; STAPHYLOCOCCUS AUREUS;

EID: 84939160343     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0655-8     Document Type: Article

References (56)

1. Weiner J 3rd, Beaussart F, Bornberg-Bauer E. Domain deletions and substitutions in the modular protein evolution. FEBS J. 2006;273:2037-47.
2. Buljan M, Frankish A, Bateman A. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol. 2010;11:R74.
3. Kim R, Guo JT. Systematic analysis of short internal indels and their impact on protein folding. BMC Struct Biol. 2010;10:24.
4. Hormozdiari F, Salari R, Hsing M, Schonhuth A, Chan SK, Sahinalp SC, et al. The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study. J Comput Biol. 2009;16:159-67.
5. Sandhya S, Rani SS, Pankaj B, Govind MK, Offmann B, Srinivasan N, et al. Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One. 2009;4:e4981.
6. Pascarella S, Argos P. Analysis of insertions/deletions in protein structures. J Mol Biol. 1992;224:461-71.
7. Taylor MS, Ponting CP, Copley RR. Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res. 2004;14:555-66.
8. Dessailly BH, Redfern OC, Cuff AL, Orengo CA. Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification. Structure. 2010;18:1522-35.
9. Nardini M, Pesce A, Milani M, Bolognesi M. Protein fold and structure in the truncated (2/2) globin family. Gene. 2007;398:2-11.
10. Grishin NV. Fold change in evolution of protein structures. J Struct Biol. 2001;134:167-85.
11. Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, et al. Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. BMC Bioinformatics. 2014;15:75.
12. Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, et al. Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol. 2002;322:841-9.
13. Triant DA, Pearson WR. Most partial domains in proteins are alignment and annotation artifacts. Genome Biol. 2015.
14. Moore SA, James MN. Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution. J Mol Biol. 1995;249:195-214.
15. Kita A, Kasai S, Miyata M, Miki K. Structure of flavoprotein FP390 from a luminescent bacterium Photobacterium phosphoreum refined at 2.7 A resolution. Acta Crystallogr D Biol Crystallogr. 1996;52:77-86.
16. Moore SA, James MN, O'Kane DJ, Lee J. Crystal structure of a flavoprotein related to the subunits of bacterial luciferase. EMBO J. 1993;12:1767-74.
17. Moore SA, James MN. Common structural features of the luxF protein and the subunits of bacterial luciferase: evidence for a (beta alpha)8 fold in luciferase. Protein Sci. 1994;3:1914-26.
18. Waddle JJ, Johnston TC, Baldwin TO. Polypeptide folding and dimerization in bacterial luciferase occur by a concerted mechanism in vivo. Biochemistry. 1987;26:4917-21.
19. Martinez-Blanco H, Reglero A, Rodriguez-Aparicio LB, Luengo JM. Purification and biochemical characterization of phenylacetyl-CoA ligase from Pseudomonas putida. A specific enzyme for the catabolism of phenylacetic acid. J Biol Chem. 1990;265:7084-90.
20. Shah MB, Ingram-Smith C, Cooper LL, Qu J, Meng Y, Smith KS, et al. The 2.1 A crystal structure of an acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates. Proteins. 2009;77:685-98.
21. Gulick AM, Lu X, Dunaway-Mariano D. Crystal structure of 4-chlorobenzoate:CoA ligase/synthetase in the unliganded and aryl substrate-bound states. Biochemistry. 2004;43:8670-9.
22. Conti E, Franks NP, Brick P. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure. 1996;4:287-98.
23. Lee TV, Johnson LJ, Johnson RD, Koulman A, Lane GA, Lott JS, et al. Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. J Biol Chem. 2010;285:2415-27.
24. Reger AS, Wu R, Dunaway-Mariano D, Gulick AM. Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry. 2008;47:8016-25.
25. Law A, Boulanger MJ. Defining a structural and kinetic rationale for paralogous copies of phenylacetate-CoA ligases from the cystic fibrosis pathogen Burkholderia cenocepacia J2315. J Biol Chem. 2011;286:15577-85.
26. Bos JL, Rehmann H, Wittinghofer A. GEFs and GAPs: critical elements in the control of small G proteins. Cell. 2007;129:865-77.
27. Daumke O, Weyand M, Chakrabarti PP, Vetter IR, Wittinghofer A. The GTPase-activating protein Rap1GAP uses a catalytic asparagine. Nature. 2004;429:197-201.
28. Scrima A, Thomas C, Deaconescu D, Wittinghofer A. The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues. EMBO J. 2008;27:1145-53.
29. Brugarolas P, Duguid EM, Zhang W, Poor CB, He C. Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr. 2011;67:707-15.
30. Kim S, Gu SA, Kim YH, Kim KJ. Crystal structure and thermodynamic properties of d-lactate dehydrogenase from Lactobacillus jensenii. Int J Biol Macromol. 2014;68:151-7.
31. Tishkov VI, Matorin AD, Rojkova AM, Fedorchuk VV, Savitsky PA, Dementieva LA, et al. Site-directed mutagenesis of the formate dehydrogenase active centre: role of the His332-Gln313 pair in enzyme catalysis. FEBS Lett. 1996;390:104-8.
32. Kanai A, Oida H, Matsuura N, Doi H. Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochem J. 2003;372:253-61.
33. Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature. 2005;437:1187-91.
34. Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, et al. The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation. Structure. 2008;16:1238-44.
35. Beg QK, Kapoor M, Mahajan L, Hoondal GS. Microbial xylanases and their industrial applications: a review. Appl Microbiol Biotechnol. 2001;56:326-38.
36. Polizeli ML, Rizzatti AC, Monti R, Terenzi HF, Jorge JA, Amorim DS. Xylanases from fungi: properties and industrial applications. Appl Microbiol Biotechnol. 2005;67:577-91.
37. Biely P, Kratky Z, Vrsanska M, Urmanicova D. Induction and inducers of endo-1,4-beta-xylanase in the yeast Cryptococcus albidus. Eur J Biochem. 1980;108:323-9.
38. Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, et al. Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1. Biochem Biophys Res Commun. 2010;403:214-9.
39. Biely P, Kratky Z, Vrsanska M. Substrate-binding site of endo-1,4-beta-xylanase of the yeast Cryptococcus albidus. Eur J Biochem. 1981;119:559-64.
40. Zmasek CM, Godzik A. Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol. 2011;12:R4.
41. Nasir A, Kim KM, Caetano-Anolles G. Global patterns of protein domain gain and loss in superkingdoms. PLoS Comput Biol. 2014;10:e1003452.
42. Pace CN, Fu H, Fryar KL, Landua J, Trevino SR, Shirley BA, et al. Contribution of hydrophobic interactions to protein stability. J Mol Biol. 2011;408:514-28.
43. Kumar S, Nussinov R. Close-range electrostatic interactions in proteins. Chembiochem. 2002;3:604-17.
44. Randles LG, Lappalainen I, Fowler SB, Moore B, Hamill SJ, Clarke J. Using model proteins to quantify the effects of pathogenic mutations in Ig-like proteins. J Biol Chem. 2006;281:24216-26.
45. Bhaskara RM, Srinivasan N. Stability of domain structures in multi-domain proteins. Sci Rep. 2011;1:40.
46. Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science. 2000;289:1546-50.
47. Birzele F, Csaba G, Zimmer R. Alternative splicing and protein structure evolution. Nucleic Acids Res. 2008;36:550-8.
48. Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, et al. The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A. 2007;104:5495-500.
49. Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, et al. Increase of functional diversity by alternative splicing. Trends Genet. 2003;19:124-8.
50. Gruszka DT, Wojdyla JA, Bingham RJ, Turkenburg JP, Manfield IW, Steward A, et al. Staphylococcal biofilm-forming protein has a contiguous rod-like structure. Proc Natl Acad Sci U S A. 2012;109:E1011-8.
51. Schroder M, Kaufman RJ. The mammalian unfolded protein response. Annu Rev Biochem. 2005;74:739-89.
52. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222-30.
53. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605-12.
54. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39:W29-37.
55. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772-80.
56. Sonnhammer EL, Hollich V. Scoredist: a simple and robust protein sequence distance estimator. BMC Bioinformatics. 2005;6:108.