The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold

Journal of Molecular Biology

Volumn 408, Issue 2, 2011, Pages 291-303

  Setiyaputra, Surya ^a   MacKay, Joel P ^a   Patrick, Wayne M ^b  

^a UNIVERSITY OF SYDNEY   (Australia)

^b MASSEY UNIVERSITY   (New Zealand)

Author keywords

NMR; protein evolution; protein structure; subdomain

Indexed keywords

HOMODIMER; ISOMERASE; MONOMER; N (5' PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE; PHOSPHORIBOSYLANTHRANILATE ISOMERASE; SOLVENT; UNCLASSIFIED DRUG;

ARTICLE; BARREL FOLD; GENETIC ANALYSIS; HYDROPHOBICITY; ISOLATION PROCEDURE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; STRUCTURE ANALYSIS;

EID: 79953675666     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.02.048     Document Type: Article

References (54)

1. 8-barrel enzyme fold Chem. Rev. 105 2005 4038 4055 (Pubitemid 41724068)
2. Nagano N., Orengo C.A., and Thornton J.M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions J. Mol. Biol. 321 2002 741 765
3. Caetano-Anollés G., Kim H.S., and Mittenthal J.E. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture Proc. Natl Acad. Sci. USA 104 2007 9358 9363 (Pubitemid 47185784)
4. Wierenga R.K. The TIM-barrel fold: a versatile framework for efficient enzymes FEBS Lett. 492 2001 193 198 (Pubitemid 32217827)
5. Brändén C.I. The TIM barrel-the most frequently occurring folding motif in proteins Curr. Opin. Struct. Biol. 1 1991 978 983
6. 8-barrel enzymes Curr. Opin. Chem. Biol. 7 2003 252 264
7. Rice P.A., Goldman A., and Steitz T.A. A helix-turn-strand structural motif common in α-β proteins Proteins 8 1990 334 340
8. Söding J., and Lupas A.N. More than the sum of their parts: on the evolution of proteins from peptides BioEssays 25 2003 837 846 (Pubitemid 37081749)
9. Lang D., Thoma R., Henn-Sax M., Sterner R., and Wilmanns M. Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion Science 289 2000 1546 1550
10. 8-barrel enzyme into two folded halves Nat. Struct. Biol. 8 2001 32 36 (Pubitemid 32043024)
11. 4-half-barrels Proc. Natl Acad. Sci. USA 101 2004 16448 16453 (Pubitemid 39557733)
12. 8-barrel protein designed from identical half barrels J. Mol. Biol. 372 2007 114 129 (Pubitemid 47223222)
13. 8-barrel protein designed from identical half-barrels Biochemistry 48 2009 1145 1147
14. 8-barrel protein scaffolds Proc. Natl Acad. Sci. USA 106 2009 3704 3709
15. 8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds J. Mol. Biol. 398 2010 763 773
16. Bertolaet B.L., and Knowles J.R. Complementation of fragments of triosephosphate isomerase defined by exon boundaries Biochemistry 34 1995 5736 5743
17. 8 barrel J. Mol. Biol. 324 2002 1031 1040
18. Higgins W., Fairwell T., and Miles E.W. An active proteolytic derivative of the α subunit of tryptophan synthase. Identification of the site of cleavage and characterization of the fragments Biochemistry 18 1979 4827 4835
19. Zitzewitz J.A., and Matthews C.R. Molecular dissection of the folding mechanism of the α subunit of tryptophan synthase: an amino-terminal autonomous folding unit controls several rate-limiting steps in the folding of a single domain protein Biochemistry 38 1999 10205 10214
20. Sánchez del Pino M.M., and Fersht A.R. Nonsequential unfolding of the α/β barrel protein indole-3-glycerol-phosphate synthase Biochemistry 36 1997 5560 5565 (Pubitemid 27200054)
21. 8 barrels J. Mol. Biol. 320 2002 1119 1133 (Pubitemid 34808828)
22. 8-barrel N-(5′- phosphoribosyl)anthranilate isomerase from Escherichia coli Biochemistry 33 1994 6350 6355 (Pubitemid 24190791)
23. Eder J., and Kirschner K. Stable substructures of eightfold βα-barrel proteins: fragment complementation of phosphoribosylanthranilate isomerase Biochemistry 31 1992 3617 3625
24. 8-barrel fold J. Mol. Biol. 382 2008 458 466
25. Patrick W.M., and Blackburn J.M. In vitro selection and characterization of a stable subdomain of phosphoribosylanthranilate isomerase FEBS J. 272 2005 3684 3697 (Pubitemid 41021180)
26. Wilmanns M., Priestle J.P., Niermann T., and Jansonius J.N. Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 Å resolution J. Mol. Biol. 223 1992 477 507
27. + binding to perdeuterated MurB: backbone atom NMR assignments and chemical-shift changes J. Mol. Biol. 267 1997 1223 1246 (Pubitemid 27192634)
28. Güntert P., Mumenthaler C., and Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA J. Mol. Biol. 273 1997 283 298 (Pubitemid 27460230)
29. Brunger A.T. Version 1.2 of the crystallography and NMR system Nat. Protoc. 2 2007 2728 2733
30. Shen Y., Delaglio F., Cornilescu G., and Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44 2009 213 223
31. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
32. Patrick W.M., and Matsumura I. A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase J. Mol. Biol. 377 2008 323 336
33. 8-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates Biochemistry 41 2002 12032 12042
34. Richardson J.S., Richardson D.C., Tweedy N.B., Gernert K.M., Quinn T.P., and Hecht M.H. Looking at proteins: representations, folding, packing, and design Biophys. J. 63 1992 1185 1209
35. Richardson J.S., and Richardson D.C. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation Proc. Natl Acad. Sci. USA 99 2002 2754 2759 (Pubitemid 34240533)
36. Wang W., and Hecht M.H. Rationally designed mutations convert de novo amyloid-like fibrils into monomeric β-sheet proteins Proc. Natl Acad. Sci. USA 99 2002 2760 2765 (Pubitemid 34240534)
37. 8 barrel motif of the alpha subunit of tryptophan synthase Protein Sci. 16 2007 1398 1409 (Pubitemid 46984874)
38. Yang X., Kathuria S.V., Vadrevu R., and Matthews C.R. βα-Hairpin clamps brace βαβ modules and can make substantive contributions to the stability of TIM barrel proteins PLoS One 4 2009 e7179
39. Höcker B., Schmidt S., and Sterner R. A common evolutionary origin of two elementary enzyme folds FEBS Lett. 510 2002 133 135 (Pubitemid 34093811)
40. Usher K.C., de la Cruz A.F., Dahlquist F.W., Swanson R.V., Simon M.I., and Remington S.J. Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability Protein Sci. 7 1998 403 412 (Pubitemid 28092862)
41. Bharat T.A., Eisenbeis S., Zeth K., and Höcker B. A βα-barrel built by the combination of fragments from different folds Proc. Natl Acad. Sci. USA 105 2008 9942 9947
42. 8 barrel fold Proc. Natl Acad. Sci. USA 98 2001 3092 3097
43. Binz H.K., Amstutz P., and Plückthun A. Engineering novel binding proteins from nonimmunoglobulin domains Nat. Biotechnol. 23 2005 1257 1268 (Pubitemid 41486853)
44. Gebauer M., and Skerra A. Engineered protein scaffolds as next-generation antibody therapeutics Curr. Opin. Chem. Biol. 13 2009 245 255
45. Kun Á., Santos M., and Szathmáry E. Real ribozymes suggest a relaxed error threshold Nat. Genet. 37 2005 1008 1011 (Pubitemid 43086161)
46. Poole A.M. Getting from an RNA world to modern cells just got a little easier BioEssays 28 2006 105 108
47. Eigen M., and Schuster P. The hypercycle. A principle of natural self-organization. Part A: emergence of the hypercycle Naturwissenschaften 64 1977 541 565 (Pubitemid 8215838)
48. Nicolet Y., and Drennan C.L. AdoMet radical proteins-from structure to evolution-alignment of divergent protein sequences reveals strong secondary structure element conservation Nucleic Acids Res. 32 2004 4015 4025 (Pubitemid 39199093)
49. Heinz D.W., Essen L.O., and Williams R.L. Structural and mechanistic comparison of prokaryotic and eukaryotic phosphoinositide-specific phospholipases C J. Mol. Biol. 275 1998 635 650 (Pubitemid 28064207)
50. Denesyuk A.I., Denessiouk K.A., Korpela T., and Johnson M.S. Functional attributes of the phosphate group binding cup of pyridoxal phosphate-dependent enzymes J. Mol. Biol. 316 2002 155 172 (Pubitemid 34729273)
51. Straus D., and Gilbert W. Genetic engineering in the Precambrian: structure of the chicken triosephosphate isomerase gene Mol. Cell. Biol. 5 1985 3497 3506
52. Gronenborn A.M., and Clore G.M. Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy Crit. Rev. Biochem. Mol. Biol. 30 1995 351 385
53. α J-couplings in staphylococcal nuclease J. Biomol. NMR 4 1994 193 200
54. Nederveen A.J., Doreleijers J.F., Vranken W., Miller Z., Spronk C.A., and Nabuurs S.B. RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank Proteins 59 2005 662 672 (Pubitemid 40695843)