The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: A three-helix bundle stabilized by zinc

Current Biology

Volumn 7, Issue 10, 1997, Pages 739-746

  Eijkelenboom, Astrid P A M ^a   Van Den Ent, Fusinita M I ^b   Vos, Arnold ^b   Doreleijers, Jurgen F ^a   Hård, Karl ^a,c   Tullius, Thomas D ^a,d,e   Plasterk, Ronald H A ^b   Kaptein, Robert ^a   Boelens, Rolf ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NETHERLANDS CANCER INSTITUTE   (Netherlands)

^c ASTRAZENECA R AND D   (Sweden)

^d Boston University ^*  (United States)

^e JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031260521     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-9822(06)00332-0     Document Type: Article

References (55)

1. Goff SP: Genetics of retroviral integration. Annu Rev Genet 1992, 26:527-544.
2. Whitcomb JM, Hughes SH: Retroviral reverse transcription and integration: progress and problems. Annu Rev Cell Biol 1992, 8:275-306.
3. Vink C, Plasterk RH: The human immunodeficiency virus integrase protein. Trends Genet 1993, 9:433-438.
4. Katz RA, Skalka AM: The retroviral enzymes. Annu Rev Biochem 1994, 63:113-173.
5. Engelman A, Craigie R: Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J Virol 1992, 66:6361-6369.
6. Bushman FD, Engelman A, Palmer I, Wingfield P, Craigie R: Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci USA 1993, 90:3428-3432.
7. Vink C, Oude Groeneger AM, Plasterk RH: Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type 1 integrase protein. Nucleic Acids Res 1993, 21:1419-1425.
8. van Gent DC, Vink C, Oude Groeneger AM, Plasterk RH: Complementation between HIV integrase proteins mutated in different domains. EMBO J 1993, 12:3261-3267.
9. Engelman A, Bushman FD, Craigie R: Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex. EMBO J 1993, 12:3269-3275.
10. Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR: Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 1994, 266:1981-1986.
11. Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM: High resolution structure of the catalytic domain of avian sarcoma virus integrase. J Mol Biol 1995, 253:333-346.
12. Yang W, Steitz TA: Recombining the structures of HIV integrase, RuvC and RNase H. Structure 1995, 3:131-134.
13. Rice P, Craigie R, Davies DR: Retroviral integrases and their cousins. Curr Opin Struct Biol 1996, 6:76-83.
14. Mizuuchi K: Polynucleotidyl transfer reactions in site-specific DNA recombination. Genes to Cells 1997, 2:1-12.
15. Eijkelenboom AP, Puras Lutzke RA, Boelens R, Plasterk RH, Kaptein R, Hård K: The DNA-binding domain of HIV-1 integrase has an SH3-like fold. Nature Struct Biol 1995, 2:807-810.
16. Lodi PJ, Ernst JA, Kuszewski J, Hickman AB, Engelman A, Craigie R, et al.: Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry 1995, 34:9826-9833.
17. Johnson MS, McClure MA, Feng DF, Gray J, Doolittle RF: Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc Natl Acad Sci USA 1986, 83:7648-7652.
18. Doolittle RF, Feng DF, Johnson MS, McClure MA: Origins and evolutionary relationships of retroviruses. Q Rev Biol 1989, 64:1-30.
19. Khan E, Mack JP, Katz RA, Kulkosky J, Skalka AM: Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res 1991, 19:851-860.
20. Burke CJ, Sanyal G, Bruner MW, Ryan JA, LaFemina RL, Robbins HL et al.: Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. J Biol Chem 1992, 267:9639-9644.
21. McEuen AR, Edwards B, Koepke KA, Ball AE, Jennings BA, Wolstenholme AJ, et al.: Zinc binding by retroviral integrase. Biochem Biophys Res Commun 1992, 189:813-818.
22. Zheng R, Jenkins TM, Craigie R: Zinc folds the amino-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity. Proc Natl Acad Sci USA 1996, 93:13659-13664.
23. 2+-dependent 3′-processing activity of human immunodeficiency virus type 1 integrase in vitro. Biochemistry 1996, 35:3837-3844.
24. 2+ promotes the self-association of human immunodeficiency virus type-1 integrase in vitro. Biochemistry 1997, 36:173-180.
25. van Gent DC, Oude Groeneger AM, Plasterk RH: Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc Natl Acad Sci USA 1992, 89:9598-9602.
26. Vincent KA, Ellison V, Chow SA, Brown PO: Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations. J Virol 1993, 67:425-437.
27. Klug A, Rhodes D: Zinc fingers: a novel protein fold for nucleic acid recognition. Trends Biochem Sci 1987, 12:464-469.
28. Kaptein R: Zinc fingers. Curr Opin Struct Biol 1991, 1:63-70.
29. Schwabe JW, Klug A: Zinc mining for protein domains. Nature Struct Biol 1994, 1:345-349.
30. Berg JM, Shi Y: The galvanization of biology: a growing appreciation for the roles of zinc. Science 1996, 271:1081-1085.
31. Pelton JG, Torchia DA, Meadow ND, Roseman S: Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques. Protein Sci 1993, 2:543-558.
32. Laskowski RA, Rullman JA, MacArthur MW, Kaptein R, Thornton JM: AQUA and PROCHECK-NMR: Programs for checking the stereochemical quality of protein structures solved by NMR. J Biomol NMR 1996, 8:477-486.
33. Chakrabarti P: Geometry of interaction of metal ions with histidine residues in protein structures. Protein Eng 1990, 4:57-63.
34. Perez-Alvarado GC, Miles C, Michelsen JW, Louis HA, Winge DR, Beckerle MC, Summers MF: Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP. Nature Struct Biol 1994, 1:388-398.
35. 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger. J Mol Biol 1994, 237:201-211.
36. Borden KL, Lally JM, Martin SR, O'Reilly NJ, Etkin LD, Freemont PS: Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development. EMBO J 1995, 14:5947-5956.
37. Holm L, Sander C: Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-138.
38. Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
39. Lawson CL: An atomic view of the I-tryptophan binding site of trp repressor. Nature Struct Biol 1996, 3:986-987.
40. Xu W, Rould MA, Jun S, Desplan C, Pabo CO: Crystal structure of a paired domain-DNA complex at 2.5 Å resolution reveals structural basis for Pax developmental mutations. Cell 1995, 80:639-650.
41. Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW: Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc Natl Acad Sci USA 1992, 89:9257-9261.
42. van Pouderoyen G, Kettting RF, Perrakis A, Plasterk RH, Sixma TK: Crystal structure of the specific DNA binding domain of Tc3 transposase of C. elegans in complex with transposon DNA. EMBO J 1997, in press.
43. Mazumder AN, Neamati JO, Ojwang S, Sunder S, Rando RF, Pommier Y: Inhibition of human immonodeficiency virus type 1 integrase by guanosine quartet structures. Biochemistry 1996, 35:13762-13771.
44. Ellison V, Gerton J, Vincent KA, Brown, PO: An essential interaction between distinct domains of of HIV-1 integrase mediates assembly of the active multimer. J Biol Chem 1995, 270:3320-3326.
45. Bizub-Bender D, Kulkosky J, Skalka AM: Monoclonal antibodies against HIV type 1 integrase: clues to molecular structure. AIDS Res Hum Retrovirus 1994, 10:1105-1115.
46. Cai M, Zheng R, Caffrey M, Craigie R, Clore GM, Gronenborn AM: Solution structure of the amino-terminal zinc binding domain of HIV-1 integrase. Nature Struct Biol 1997, 4:567-577.
47. van Gent DC, Elgersma Y, Bolk MW, Vink C, Plasterk RH: DNA binding properties of the integrase proteins of human immunodeficiency viruses types 1 and 2. Nucleic Acids Res 1991, 19:3821-3827.
48. Zuiderweg ERP: A proton-detected heteronuclear chemical-shift correlation experiment with improved resolution and sensitivity. J Magn Reson 1990, 86:346-357.
49. Folkers PJ, Folmer RH, Konings RN, Hilbers CW: Overcoming the ambiguity problem encountered in the analysis of nuclear Overhauser magnetic resonance spectra of symmetric dimer proteins. J Am Chem Soc 1993, 115:3798-3799.
50. 15N isotope editing of biomolecular complexes. Application to a mutant lac repressor headpiece DNA complex. J Magn Res B 1996, 111:199-203.
51. Brünger AT: X-PLOR, version 3.1: a system for X-ray crystallography and NMR. Yale University Press: New Haven, CT, USA; 1992.
52. Fletcher CM, Jones DN, Diamond R, Neuhaus D: Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J Biomol NMR 1996, 8:292-310.
53. Nilges M, Clore GM, Gronenborn AM: Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. Circumventing problems associated with folding. FEBS Lett 1988, 239:129-136.
54. Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
55. Koradi R, Billeter M, Wüthrich K: MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996, 14:51-55.