Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins

Proteins: Structure, Function and Genetics

Volumn 37, Issue 3, 1999, Pages 485-493

  Brody, S S ^a   Gough, S P ^a   Kannangara, C G ^a  

^a CARLSBERG LABORATORY   (Denmark)

Author keywords

Coiled coil; Glutamyl tRNA reductase; Hordeum vulgare; Mg; Protein structure prediction; Thioester formation

Indexed keywords

GLUTAMIC ACID DERIVATIVE; GLUTAMIC ACID TRANSFER RNA; MAGNESIUM; OXIDOREDUCTASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; SUCCINYL COENZYME A SYNTHETASE;

ARTICLE; BINDING SITE; CONTROLLED STUDY; ENZYME MECHANISM; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALDEHYDE OXIDOREDUCTASES; AMINO ACID SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; HEME; HORDEUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NADP; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID;

HORDEUM VULGARE;

EID: 0032750527     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991115)37:3<485::AID-PROT15>3.0.CO;2-G     Document Type: Article

References (47)

1. Kannangara C, Gough SP, Bruyant P, Hoober JK, Kahn A, von Wettstein D. TRNAGlu as a cofactor in delta-aminolevulinate biosynthesis steps that regulate chlorophyll synthesis. Trends Biochem Sci 1988;13:139-143.
2. Glu reductase in Escherichia coli as a fusion protein with glutathione S-transferase. Proc Natl Acad Sci USA 1996;93:9287-9291.
3. Crawford IP, Niermann T, Kirschner K. Predictions of secondary structure by evolutionary comparison: application to the alpha-subunit of tryptophan synthase. Proteins 1987;1:118-129.
4. Edwards YJK, Perkins SJ. The protein fold of the von Willbrand factor type A is predicted to be similar to the open twisted β-sheet flanked by α-helices found in human ras-p21. FEBS Lett 1995;358: 283-286.
5. Gerloff DL, Chelvanayagam G, Benner SA. A predicted consensus structure for the protein-kinase c2 homology (c2h) domain, the repeating unit of synaptotagmin. Proteins 1995;22:229-310.
6. Bazan JF. Structure design and molecular evolution of a cytokine receptor superfamily. Proc Nat Acad Sci USA 1990;87:6934-6938.
7. Miller RT, Jones DT, Thornton JM. Protein fold recognition by sequence threading: tools and assessment techniques. FASEB J 1996;10:171-178.
8. Wisconsin Package, version 8, Madison, WI, Sept 1994. Program manual for EGCG package, Peter Rice, Cambridge, UK, The Sanger Centre, Hinxton Hall, Aug 1995.
9. Levin JM, Robson B, Garnier J. An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Lett 1986;205:303-308.
10. Deleage G, Roux B. An algorithm for protein secondary structure prediction based on class prediction. Protein Eng 1987;1:289-294.
11. Geourjon C, Deleage G. SOPM -a self-optimised method for protein secondary structure prediction. Protein Eng 1994;7:157-164.
12. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
13. Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 1994;19:55-72.
14. Gibrat J-F, Garnier J, Robson B. Further developments of the protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J Mol Biol 1987;198:425-443.
15. Rost B, Burkhard H. TOPITS: threading one-dimensional predictions into three-dimensional structures. In: Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S, editors. The third international conference on Intelligent Systems for Molecular Biology (ISMB), Cambridge, U.K., Jul 16-19. Menlo Park, CA: AAAI Press; 1995. p 314-321 and (www.expasy.ch/www/tools. html)
16. Jones DT, Miller RT, Thornton JM. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins 1995;23:387-397.
17. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
18. Lupas A, Van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science 1991;252:1162-1164.
19. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spacial restraints. J Mol Biol 1993;234:779-815.
20. Livingstone CD, Barton GJ. Secondary structure prediction from multiple sequence data: blood clotting factor XIII and Yersinia protein-tyrosine phosphatase. Int J Peptide Protein Res 1994;44: 239-244.
21. Zvelebil MJJM, Barton GJ, Taylor WR, Steinberg MJE. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol 1987;195:957-961.
22. Brenner SA, Gerloff D. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. Adv Enzyme Res 1990;31:121-181.
23. Wolodko WT, Fraser ME, James MN, Bridger WA. The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-Å resolution. J Biol Chem 1994;269:10883-10890.
24. Lemer CM, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. Protein 1996;23:337-355.
25. Branden C, Tooze J. Introduction to protein structure. New York:Garland; 1991. p 144-152.
26. Rossmann MG, Liljas A, Branden CI, Banaszak LJ. Evolutionary and structural relationships among dehydrogenases. In: Boyer PD, editor. The enzymes, XI. New York: Academic Press; 1975. p 61-102.
27. Rossmann MG, Adams MJ, Buehner M, et al. Structural constraints of possible mechanisms of lactate dehydrogenase as shown by high resolution studies of the apoenzyme and a variety of enzyme complexes. Cold Spring Harbor Symp Quant Biol 1972;36:179-191.
28. Bocanegra JA, Scrutton NS, Perham RN. Creation of an NADP-dependent pyruvate dehydrogenase multienzyme complex by protein engineering. Biochem 1993;32:2737-2740.
29. Ouyang J, Viola RE. Use of structural comparisons to select mutagenic targets in aspartate-beta-semialdehyde dehydrogenase. Biochemistry 1995;34:6394-6399.
30. Scrutton NS, Berry A, Perham RW. Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature 1990;343:38-43.
31. Mittl PR, Berry A, Scrutton NS, Perham RN, Schulz GE. Anatomy of an engineered NAD-binding site. Protein Sci 1994;3:1504-1514.
32. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
33. Kannangara C, Gough SP, Oliver RP, Rasmussen SK. Biosynthesis of delta-aminoevulinate in greening barley leaves VI activation of glutamate by ligation to RNA. Carlsberg Res Commun 1984;49: 417-437.
34. Willows RD, Kannangara CG, Pontoppidan B. Nucleotides of tRNA (Glu) involved in recognition by barley chloroplast glutamyl-tRNA synthetase and glutamyl tRNA reductase. Biochim Biophys Acta 1995;1263:228-234.
35. Rould MA, Perona JJ, Steitz TA. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 1991;18:352: 213-218.
36. Farber GK, Pretsko GA. The evolution of alpha/beta barrel enzymes. TIBS 1990;15:228-234.
37. Biesecker G, Harris JI, Thierry JC, Walker JE, Wonacott AJ. Sequence and structure of D-glyceraldehyde 3-phosphate dehydrogenase from Bacillus stearothermophilus. Nature 1977;266:328-333.
38. Kim H, Feil IK, Verlinde CL, Petra PH, Hol WG. Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site. Biochemistry 1995;34:14975-14986.
39. Thoden JB, Miran SG, Phillips JC, Howard AJ, Raushel FM, Holden HM. Carbamoyl phosphate synthase: caught in the act of glutamine hydrolysis. Biochemistry 1998;37:8825-8831.
40. Pontoppidan G, Kannangara CG. Purification and partial characterisation of barley glutamyl-tRNAGlu reductase, the enzyme that directs glutamate to chlorophyll biosynthesis. Eur J Biochem 1994;225:529-537.
41. Huang DD, Wang WY. Chlorophyll biosynthesis in Chlamydomonas starts with the formation of glutamyl-tRNA. J Biol Chem 1986;261:13451-13455.
42. Jahn D. Complex formation between glutamyl-tRNA synthetase and glutamyl-tRNA reductase during the tRNA-dependent synthesis of 5-aminolevulinic acid in Chlamydomonas reinhardtii. FEBS Lett 1992;314:77-80.
43. Chen W, Wright L, Li S, Cosloy SD, Russell CS. Expression of glutamyl-tRNA reductase in Escherichia coli. Biochim Biophys Acta 1996;1309:109-121.
44. Schroder I, Hederstedt L, Kannangara CG, Gough SP. Glutamyl-tRNA reductase activity in Bacillus subtilis is dependent on the hemA gene product. Biochem J 1992;281:843-850.
45. Rieble S, Beale SI. Purification of glutamyl-tRNA reductase from Synechocystis sp. PCC 6803. J Biol Chem 1991;266:9740-9745.
46. Verkamp E, Jahn M, Jahn D, Kumar AM, Soll D. Glutamyl-tRNA reductase from Escherichia coli and Synechocystis 6803. Gene structure and expression. J Biol Chem 1992;25:8275-8280.
47. Lukatela G, Krauss N, Theis K, et al.Crystal structure of human arylsulfatase A: the aldehyde function and the metal ion at the active site suggest a novel mechanism for sulfate ester hydrolysis. Biochemistry 1998;37:3654-3664.