Protein fold irregularities that hinder sequence analysis

Current Opinion in Structural Biology

Volumn 8, Issue 3, 1998, Pages 364-371

  Russell, Robert B ^a   Ponting, Chris P ^b  

^a GLAXOSMITHKLINE   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; EVOLUTION; PREDICTION; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION;

EID: 0032103855     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80071-7     Document Type: Article

References (70)

1. Doolittle RF. The multiplicity of domains in proteins. Annu Rev Biochem. 64:1995;287-314.
2. Bork P, Gibson TJ. Applying motif and profile searches. Methods Enzymol. 266:1996;162-184.
3. Heringa J, Taylor WR. Three-dimensional domain duplication, swapping and stealing. Curr Opin Struct Biol. 7:1997;416-421.
4. Russell RB. Domain insertion. Protein Eng. 7:1994;1407-1410.
5. Lindqvist Y, Schreider G. Circular permutation of natural protein sequences: structural evidence. Curr Opin Struct Biol. 7:1997;422-427.
6. Fletterick RJ, Bazan JF. When one and one are not two. Nat Struct Biol. 2:1995;721-723.
7. Zhang G, Liu Y, Ruono AE, Hurley JH. Structure of the adenylyl cyclase catalytic core. of outstanding interest Nature. 386:1997;247-253 See annotation by Artymiuk et al. 1997 [8].
8. Artymiuk PJ, Poirrette AR, Rice DW, Willet P. A polymerase I palm in adenylyl cyclase? of outstanding interest Nature. 388:1997;33-34 The authors describe a structural similarity between acenylyl cyclase [7] and the DNA polymerase palm domain. There is little sequence similarity between the two proteins, although a similar reaction mechanism and key residue conservation suggest that the cyclase contains only the palm domain (i.e. the catalytic centre) of polymerases. Additions to the fold seen in polymerases serve mostly to regulate binding and specificity; different domain additions (not insertions) to cyclases (such as a second catalytic domain and transmembrane regions) modify function and cellular location.
9. Doublié S, Tabor S, Long AM, Richardson CC, Ebenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. of special interest Nature. 391:1997;251-258 The relative orientations of domains in DNA polymerases appear to be crucial to their function. Bacteriophage T7 DNA polymerase contains a 71 residue thioredoxin-binding domain, inserted into the tip of the thumb, that mediates a thioredoxin-dependent increase in processive DNA synthesis.
10. Åberg A, Yaremchuk A, Tukalo M, Rasmussen B, Cusack S. Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. of special interest Biochemistry. 36:1997;3084-3094 In common with other class II synthetases. T. thermophilus histidyl-tRNA synthetase contains a domain insert that might assist in tRNA binding. The corresponding domain in the previously determined structure of E. coli histidyl-tRNA synthetase was completely disordered.
11. Kostrewa D, Grüninger-Leitch F, D'Arcy A, Broger C, Mitchell D, van Loon APGM. Crystal structure of phytase from Aspergillus ficuum at 2.5 Å resolution. of special interest Nat Struct Biol. 4:1997;185-190 Phytase is similar in both sequence and structure to rat acid phosphatase (PDB accession code 1RPA). The inserted domain in phytase, which is composed of several excursions from the α/β domain, contributes to an active site that is, however, larger than that of rat acid phosphatase as a result of its preference for larger substrates.
12. Möhrle JJ, Zhao Y, Wernli B, Franklin RM, Kappes B. Molecular cloning, characterization and localization of PfPK4, an eIF-2α kinase-related enzyme from the malarial parasite Plasmodium falciparum. of special interest Biochem J. 328:1997;677-687 The protozoan protein kinase PfPK4 is closely related to mammalian eukaryotic initiation factor 2α (eIF-2α) kinases, both of which contain two inserts. The first of these is usually extended for mammalian elF-2α kinases, and is extremely long for PfPK4. No domain homologues have been detected within these inserts.
13. Essen L-O, Perisic O, Katan M, Williams RL. Crystal structure of a mammalian phosphoinositide-specific phospholipase Cδ Nature. 380:1996;595-602.
14. Musacchio A, Gibson T, Rice P, Thompson J, Saraste M. The PH domain: a common piece in the structural patchwork of signalling proteins. Trends Biochem Sci. 18:1993;343-348.
15. Ponting CP, Phillips C. DHR domains in syntrophins, neuronal NO synthases and other intracellular proteins. Trends Biochem Sci. 20:1995;102-103.
16. Leung T, Chen XQ, Manser E, Lim L. The p160 RhoA-binding kinase ROK alpha is a member of the kinase family and is involved in the reorganization of the cytoskeleton. Mol Cell Biol. 16:1996;5313-5327.
17. Zheng J, Chen R-H, Corblan-Garcia S, Cahill SM, Bar-Sagi D, Cowburn D. The solution structure of the pleckstrin homology domain of human SOS1. A possible structural role for the sequential association of diffuse B cell lymphoma and pleckstrin homology domains. of special interest J Biol Chem. 272:1997;30340-30344 Dbl-homology (DH) domains that are contained in several proto-oncogene products are invariably followed in sequence by a pleckstrin homology (PH) domain whose probable role is to recruit the protein to the cell membrane. The attempts by Cowburn and co-workers to express in E. coli a recombinant PH domain from the DH-containing SOS1 protein using commonly used domain limits from sequence analysis failed due to protein insolubility. Extending the domain at its N terminus, however, resulted in a soluble product whose structure shows a well-defined N-terminal α helix packed against an interstrand loop that is predicted to modulate the binding of inositol 1,4,5-trisphosphate.
18. Hyvönen M, Saraste M. Structure of the PH domain and Btk motif from Bruton's tyrosine kinase: molecular explanations for X-linked agammaglobulinaemia. of outstanding interest EMBO J. 16:1997;3396-3404 A large number of mutations in the gene for Bruton's tyrosine kinase (Btk) have been found in patients suffering from X-linked agammaglobulinaemia. One of these mutations results in the substitution of a conserved cysteine that coordinates zinc binding in a C-terminal extension of the PH domains of Btk-like molecules. The fold of the Btk extension appears to require the presence of the associated PH domain since it packs closely against it in the crystal structure.
19. Ponting CP, Cai Y-D, Bork P. Breast cancer gene product TSG101: a regulator of ubiquitination? of special interest J Mol Med. 75:1997;467-469 See annotation to Koonin and Abagyan 1997 [20].
20. Koonin EV, Abagyan RA. TSG101 may be the prototype of a class of dominant negative ubiquitin regulators. of special interest Nat Genet. 16:1997;330-331 TSG101 has been identified as a homologue of ubiquitin-conjugating enzymes. It appears to differ from the known structures of ubiquitin-conjugating enzymes, however, lacking their active-site cysteines and being truncated at its C terminus.
21. Musco G, Stier G, Joseph C, Morelli MAC, Nilges M, Gibson TJ, Pastore A. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Cell. 85:1996;237-245.
22. Cunningham BA, Hemperly JJ, Hopp TP, Edelman GM. Favin versus concanavalin A circularly permuted amino acid sequences. Proc Natl Acad Sci USA. 76:1979;3218-3222.
23. Yamauchi D, Minamikawa T. Structure of the gene encoding concanavalin A from C. gladiata and its expression in E. coli cells. FEBS Lett. 260:1990;127-130.
24. Goldberg DP. Circularly permuted proteins. Protein Eng. 2:1989;493-495.
25. Pan T, Uhlenbeck OC. Circularly permuted DNA, RNA and proteins - a review. Gene. 125:1993;111-114.
26. Ponting CP, Russell RB. Swaposins: circular permutations within genes encoding saposin homologues. Trends Biochem Sci. 20:1995;179-180.
27. Liepinsh E, Andersson M, Ruysschaert JM, Otting G. Saposin fold revealed by the NMR structure of NK-lysin. of special interest Nat Struct Biol. 4:1997;793-795 The first structure determination of a saposin homologue. The novel fold shows how the previously reported sequence permutation [26] can be accommodated by the tertiary structure of saposins. It appears possible to relocate the N and C termini with minimal disruption to the overall structure.
28. Guruprasad K, Tormakangas K, Kervinen J, Blundell TL. Comparative modelling of barley-grain aspartic proteinase: a structural rationale for observed hydrolytic specificity. FEBS Lett. 352:1994;131-136.
29. Flint HJ, Whitehead TR, Martin JC, Gasparic A. Interrupted catalytic domain structure in xylanases from two distantly related strains of Prevotella ruminicola. of special interest Biochim Biophys Acta. 1337:1997;161-165 A report of the structures xylanases from two strains of an anaerobic bacterium, in which the catalytic domain of one is interrupted by a domain that is distantly related to cellulose-binding domains, although permuted.
30. Murzin AG. Probable circular permutation in the favin-binding domain. of outstanding interest Nat Struct Biol. 5:1998;101 The recently solved structure of the FMN-binding protein from Desulfovibrio vulgaris [31] was proposed to share an ancient common ancestor with domains from trypsin-like serine proteinases. Structural alignment after permutation, however, reveals a closer relationship with the ferredoxin reducatase superfamily of enzymes. Seven β strands forming the core β barrel structure, an α helix, and an equivalent FAD - FMN binding site were found following circular permutation and structure superimposition.
31. Liepinsh E, Kitamura M, Murakami T, Nakaya T, Ottig G. Pathway of chymotrypsin evolution suggested by the structure of the FMN-binding protein from Desulfovibrio vulgaris. Nat Struct Biol. 4:1997;975-979.
32. Johnson PE, Joshi MD, Tomme P, Kilburn DG, McIntosh LP. Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy. Biochemistry. 35:1996;14381-14394.
33. Islam SA, Luo J, Sternberg MJE. Identification and analysis of domains in proteins. Protein Eng. 8:1995;523-525.
34. Greenblatt HM, Ryan CA, James MNG. Structure of the complex of Streptomyces griseus proteinase B and polypeptide chymotrypsin inhibitor-1 from Russet Burbank potato tubers at 2.1 Å resolution. J Mol Biol. 205:1989;201-228.
35. Taylor BH, Young RJ, Scheuring CF. Induction of a proteinase inhibitor II - a class of gene by auxin in tomato roots. Plant Mol Biol. 23:1993;1005-1014.
36. 2. Cell. 83:1995;1047-1058.
37. Bennett MJ, Schlunegger MP, Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 4:1995;2455-2468.
38. Murray AJ, Lewis SJ, Barclay AN, Brady RL. One sequence, two folds: a metastable structure of CD2. Proc Natl Acad Sci USA. 92:1995;7337-7341.
39. Piccoli R, Tamburrini M, Piccialli G, Di Donato A, Parente A, D'Alessio G. The dual-mode quaternary structure of seminal RNase. Proc Natl Acad Sci USA. 89:1992;1870-1874.
40. McGrath ME, Gillmor SA, Fletterick RJ. Ecotin: lessons on survival in a protease-filled world. Protein Sci. 4:1995;141-148.
41. Parge HE, Arvai AS, Murtari DJ, Reed SI, Tainer JA. Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control. Science. 262:1993;387-395.
42. Green SM, Gittis AG, Meeker AK, Lattman EE. One-step evolution of a dimer from a monomeric protein. Nat Struct Biol. 2:1995;746-751.
43. Ealick SE, Cook WJ, Vijay-Kumar S, Carson M, Nagabhushan TL, Trotta PP, Bugg CE. Three-dimensional structure of recombinant human interferon-γ Science. 252:1991;698-702.
44. Milburn MV, Hassell AM, Lambert MH, Jordan SR, Proudfoot AEI, Graber P, Wells TNC. A novel dimer configuration revealed by the crystal structure at 2.4 Å resolution of human interleukin-5. Nature. 363:1993;172-176.
45. Zdanov A, Schalk-Hihi C, Gustchina A, Tsang M, Weatherbee J, Wlodawer A. Crystal structure of interleukin-10 reveals the functional dimer with an unexpected topological similarity to interferon γ Structure. 3:1995;591-601.
46. Kishan KVR, Scita G, Wong WT, Di Fiore PP, Newcomer ME. The SH3 domain of Eps8 exists as a novel intertwined dimer. of outstanding interest Nat Struct Biol. 4:1997;739-743 The crystal structure of the Eps8 SH3 domain dimer shows that it is formed by β-strand exchange. The authors show using co-immunoprecipitation experiments that full length Eps8 is a dimer in vivo and that dimerisation is dependent on an intact SH3 domain. Since the SH3 domain polyproline-binding site is partially occluded in the dimer, the possibility remains that the regulation of Eps8 function may occur via SH3-mediated reversible dimerisation. Tandem domains can not always be considered to represent independent structural domains.
47. Tegoni M, Ramoni R, Bignetti E, Spinelli S, Cambillau C. Domain swapping creates a third putative combining site in bovine odorant binding protein dimer. Nat Struct Biol. 3:1996;863-867.
48. Bianchet MA, Bains G, Pelosi P, Pevsner J, Snyder SH, Monaco HL, Amzel LM. The three-dimensional structure of bovine odorant binding protein and its mechanism of odor recognition. Nat Struct Biol. 3:1996;934-939.
49. Mottonen J, Strand A, Symersky J, Sweet RM, Danley De, Geoghegan KF, Gerard RD, Goldsmith EJ. Structural basis of latency in plasminogen activator inhibitor-1. Nature. 355:1992;270-273.
50. Cooke RM, Carter BG, Murray-Rust P, Hartshorn MJ, Herzyk P, Hubbard RE. The solution structure of echistatin: evidence for disulphide bond rearrangement in homologous snake toxins. Protein Eng. 5:1992;473-477.
51. Zimmermann GR, Legault P, Selsted ME, Pardi A. Solution structure of bovine neutrophil β-defensin-12: the peptide fold of the β-defensins is identical to that of the classical defensins. Biochemistry. 34:1995;13663-13671.
52. Benitez BAS, Hunter MJ, Meininger DP, Komives EA. Structure of the fifth EGF-like domain of thrombomodulin: an EGF-like domain with a novel disulfide-bonding pattern. of outstanding interest J Mol Biol. 273:1997;913-926 The NMR structure of thrombomodulin epidermal growth factor-like domain 5 (TMEGF5) shows a different disulphide-bonding pattern from that of EGF itself. In addition, a two-stranded β sheet that is common to most EGF homologues is lacking in TMEGF5. The TMEGF5 fragment with this novel disulphide-bonding pattern retains the thrombin-binding function of intact thrombomodulin.
53. Perler FB, Davis EO, Dean GE, Gimble FS, Jack WE, Neff N, Noren CJ, Thorner J, Belfort M. Protein splicing elements: inteins and exteins - a definition of terms and recommended nomenclature. Nucleic Acids Res. 22:1994;1125-1127.
54. Perler FB. Protein splicing of inteins and hedgehog autoproteolysis: structure, function, and evolution. of outstanding interest Cell. 9:1998;1-4 An excellent review discussing the recent advances in the understanding of the structure, function and evolution of inteins.
55. Duan X, Gimble F, Quiocho F. Crystal structure of PI-SceI, a homing autoproteolysis:endonuclease with protein splicing activity. of outstanding interest Cell. 89:1997;555-564 The first view of the folds of the two domains commonly contained in inteins. Domain II is a core endonuclease that is inserted into domain I, whose fold is similar to that of the Hedgehog autoprocessing domain. Domain I also accommodates an insertion that mediates DNA recognition.
56. Klabunde T, Sharma S, Telenti A, Jacobs WR Jr, Sacchettini JC. Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing. of outstanding interest Nat Struct Biol. 5:1998;31-36 The GyrA intein differs from most inteins in lacking both the endonuclease domain and the DNA recognition region. Its structure and function are strikingly similar to those of the Hedgehog autoprocessing domain.
57. Tanaka-Hall TM, Porter JA, Young KE, Koonin EV, Beachy PA, Leahy DJ. Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins. of outstanding interest Cell. 91:1997;85-97 The first reported three-dimensional structure of an autoprocessing domain that is homologous to domain I of inteins. The structure provides insights into the mechanism of these autocatalytic modules and, together with a wider family of homologues, provides examples of domain duplication, insertion, permutation and secondary structure exchange.
58. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 215:1990;403-410.
59. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 147:1981;195-197.
60. Zuker M. Suboptimal sequence alignment in molecular biology: alignment with error analysis. J Mol Biol. 221:1991;403-420.
61. Barton GJ. An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps. Comput Appl Biosci. 9:1993;729-734.
62. Birney E, Thompson JD, Gibson TJ. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res. 24:1996;2730-2739.
63. Pearson WR. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics. 11:1991;635-650.
64. Tatusov RI, Altschul SF, Koonin EV. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci USA. 9:1994;12091-12095.
65. Neuwald AF, Liu JS, Lipman DJ, Lawrence CE. Extracting protein alignment models from the sequence database. Nucleic Acids Res. 25:1997;1665-1677.
66. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. of outstanding interest Nucleic Acids Res. 25:1997;3389-3402 Modifications to BLAST have made the method more powerful. Gapped alignment now allows more continuous domains to be identified and iterative database searches, fined tuned by the construction of profiles that are specific to a protein family, make the method more sensitive. The central assumptions of short gaps and contiguous segments mean, however, that permutations and insertions are still difficult to detect without postprocessing.
67. Searls DB, Murphy KP. Automata-theoretic models of mutation and alignment. Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. 1995;341-349 AAAI Press, Menlo Park.
68. Birney E, Durbin R. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. of special interest Ismb. 7:1997;56-64 This paper presents a method for generating a dynamic programming code that is specific to an application, given a fairly simple textural description of the problem that needs to be solved. It may not be able to detect insertions or permutations directly, although certainly the possibility exists for the construction of complex grammars specific to the task.
69. Heringa J, Argos P. A method to recognised distant repeats in protein sequences. Proteins. 17:1993;341-391.
70. Kraulis PJ. MOLSCRIPT: a program to produce detailed and schematic plots of protein structures. J Appl Crystallogr. 24:1991;950-964.