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Mol Biol Cell. Feb 1997; 8(2): 219–230.
PMCID: PMC276075

Molecular dissection of a LIM domain.

Abstract

LIM domains are novel sequence elements that are found in more than 60 gene products, many of which function as key regulators of developmental pathways. The LIM domain, characterized by the cysteine-rich consensus CX2CX16-23HX2CX2CX2CX16-21 CX2-3(C/H/ D), is a specific mental-binding structure that consists of two distinct zinc-binding subdomains. We and others have recently demonstrated that the LIM domain mediates protein-protein interactions. However, the sequences that define the protein-binding specificity of the LIM domain had not yet been identified. Because structural studies have revealed that the C-terminal zinc-binding module of a LIM domain displays a tertiary fold compatible with nucleic acid binding, it was of interest to determine whether the specific protein-binding activity of a LIM domain could be ascribed to one of its two zinc-binding subdomains. To address this question, we have analyzed the protein-binding capacity of a model LIM peptide, called zLIM1, that is derived from the cytoskeletal protein zyxin. These studies demonstrate that the protein-binding function of zLIM1 can be mapped to sequences contained within its N-terminal zinc-binding module. The C-terminal zinc-binding module of zLIM1 may thus remain accessible to additional interactive partners. Our results raise the possibility that the two structural subdomains of a LIM domain are capable of performing distinct biochemical functions.

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Selected References

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  • Archer VE, Breton J, Sanchez-Garcia I, Osada H, Forster A, Thomson AJ, Rabbitts TH. Cysteine-rich LIM domains of LIM-homeodomain and LIM-only proteins contain zinc but not iron. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):316–320. [PMC free article] [PubMed]
  • Bach I, Rhodes SJ, Pearse RV, 2nd, Heinzel T, Gloss B, Scully KM, Sawchenko PE, Rosenfeld MG. P-Lim, a LIM homeodomain factor, is expressed during pituitary organ and cell commitment and synergizes with Pit-1. Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2720–2724. [PMC free article] [PubMed]
  • Baltz R, Domon C, Pillay DT, Steinmetz A. Characterization of a pollen-specific cDNA from sunflower encoding a zinc finger protein. Plant J. 1992 Sep;2(5):713–721. [PubMed]
  • Barnes JD, Crosby JL, Jones CM, Wright CV, Hogan BL. Embryonic expression of Lim-1, the mouse homolog of Xenopus Xlim-1, suggests a role in lateral mesoderm differentiation and neurogenesis. Dev Biol. 1994 Jan;161(1):168–178. [PubMed]
  • Blanar MA, Rutter WJ. Interaction cloning: identification of a helix-loop-helix zipper protein that interacts with c-Fos. Science. 1992 May 15;256(5059):1014–1018. [PubMed]
  • Boehm T, Foroni L, Kaneko Y, Perutz MF, Rabbitts TH. The rhombotin family of cysteine-rich LIM-domain oncogenes: distinct members are involved in T-cell translocations to human chromosomes 11p15 and 11p13. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4367–4371. [PMC free article] [PubMed]
  • Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. [PubMed]
  • Crawford AW, Michelsen JW, Beckerle MC. An interaction between zyxin and alpha-actinin. J Cell Biol. 1992 Mar;116(6):1381–1393. [PMC free article] [PubMed]
  • Crawford AW, Pino JD, Beckerle MC. Biochemical and molecular characterization of the chicken cysteine-rich protein, a developmentally regulated LIM-domain protein that is associated with the actin cytoskeleton. J Cell Biol. 1994 Jan;124(1-2):117–127. [PMC free article] [PubMed]
  • Crossley M, Merika M, Orkin SH. Self-association of the erythroid transcription factor GATA-1 mediated by its zinc finger domains. Mol Cell Biol. 1995 May;15(5):2448–2456. [PMC free article] [PubMed]
  • Dahlman-Wright K, Wright A, Carlstedt-Duke J, Gustafsson JA. DNA-binding by the glucocorticoid receptor: a structural and functional analysis. J Steroid Biochem Mol Biol. 1992 Mar;41(3-8):249–272. [PubMed]
  • Dawid IB, Toyama R, Taira M. LIM domain proteins. C R Acad Sci III. 1995 Mar;318(3):295–306. [PubMed]
  • Feuerstein R, Wang X, Song D, Cooke NE, Liebhaber SA. The LIM/double zinc-finger motif functions as a protein dimerization domain. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10655–10659. [PMC free article] [PubMed]
  • Geisberg JV, Lee WS, Berk AJ, Ricciardi RP. The zinc finger region of the adenovirus E1A transactivating domain complexes with the TATA box binding protein. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2488–2492. [PMC free article] [PubMed]
  • Gill GN. The enigma of LIM domains. Structure. 1995 Dec 15;3(12):1285–1289. [PubMed]
  • Giraud-Panis MJ, Duckett DR, Lilley DM. The modular character of a DNA junction-resolving enzyme: a zinc-binding motif in bacteriophage T4 endonuclease VII. J Mol Biol. 1995 Oct 6;252(5):596–610. [PubMed]
  • Hammarström A, Berndt KD, Sillard R, Adermann K, Otting G. Solution structure of a naturally-occurring zinc-peptide complex demonstrates that the N-terminal zinc-binding module of the Lasp-1 LIM domain is an independent folding unit. Biochemistry. 1996 Oct 1;35(39):12723–12732. [PubMed]
  • Härd T, Kellenbach E, Boelens R, Maler BA, Dahlman K, Freedman LP, Carlstedt-Duke J, Yamamoto KR, Gustafsson JA, Kaptein R. Solution structure of the glucocorticoid receptor DNA-binding domain. Science. 1990 Jul 13;249(4965):157–160. [PubMed]
  • Khoo C, Cousins RJ. Purification and properties of rat cysteine-rich intestinal protein. Biochem J. 1994 Apr 15;299(Pt 2):445–450. [PMC free article] [PubMed]
  • Kosa JL, Michelsen JW, Louis HA, Olsen JI, Davis DR, Beckerle MC, Winge DR. Common metal ion coordination in LIM domain proteins. Biochemistry. 1994 Jan 18;33(2):468–477. [PubMed]
  • Jurata LW, Kenny DA, Gill GN. Nuclear LIM interactor, a rhombotin and LIM homeodomain interacting protein, is expressed early in neuronal development. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11693–11698. [PMC free article] [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Lee JS, Galvin KM, Shi Y. Evidence for physical interaction between the zinc-finger transcription factors YY1 and Sp1. Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):6145–6149. [PMC free article] [PubMed]
  • Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 1991 Aug 8;352(6335):497–505. [PubMed]
  • Merika M, Orkin SH. Functional synergy and physical interactions of the erythroid transcription factor GATA-1 with the Krüppel family proteins Sp1 and EKLF. Mol Cell Biol. 1995 May;15(5):2437–2447. [PMC free article] [PubMed]
  • Michelsen JW, Schmeichel KL, Beckerle MC, Winge DR. The LIM motif defines a specific zinc-binding protein domain. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4404–4408. [PMC free article] [PubMed]
  • Michelsen JW, Sewell AK, Louis HA, Olsen JI, Davis DR, Winge DR, Beckerle MC. Mutational analysis of the metal sites in an LIM domain. J Biol Chem. 1994 Apr 15;269(15):11108–11113. [PubMed]
  • O'Connor TR, Graves RJ, de Murcia G, Castaing B, Laval J. Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. J Biol Chem. 1993 Apr 25;268(12):9063–9070. [PubMed]
  • Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science. 1993 Jul 23;261(5120):438–446. [PubMed]
  • Osada H, Grutz G, Axelson H, Forster A, Rabbitts TH. Association of erythroid transcription factors: complexes involving the LIM protein RBTN2 and the zinc-finger protein GATA1. Proc Natl Acad Sci U S A. 1995 Oct 10;92(21):9585–9589. [PMC free article] [PubMed]
  • Pérez-Alvarado GC, Kosa JL, Louis HA, Beckerle MC, Winge DR, Summers MF. Structure of the cysteine-rich intestinal protein, CRIP. J Mol Biol. 1996 Mar 22;257(1):153–174. [PubMed]
  • Pérez-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. Nat Struct Biol. 1994 Jun;1(6):388–398. [PubMed]
  • Sadler I, Crawford AW, Michelsen JW, Beckerle MC. Zyxin and cCRP: two interactive LIM domain proteins associated with the cytoskeleton. J Cell Biol. 1992 Dec;119(6):1573–1587. [PMC free article] [PubMed]
  • Sánchez-García I, Rabbitts TH. The LIM domain: a new structural motif found in zinc-finger-like proteins. Trends Genet. 1994 Sep;10(9):315–320. [PubMed]
  • Schmeichel KL, Beckerle MC. The LIM domain is a modular protein-binding interface. Cell. 1994 Oct 21;79(2):211–219. [PubMed]
  • Seto E, Lewis B, Shenk T. Interaction between transcription factors Sp1 and YY1. Nature. 1993 Sep 30;365(6445):462–464. [PubMed]
  • Shawlot W, Behringer RR. Requirement for Lim1 in head-organizer function. Nature. 1995 Mar 30;374(6521):425–430. [PubMed]
  • Stronach BE, Siegrist SE, Beckerle MC. Two muscle-specific LIM proteins in Drosophila. J Cell Biol. 1996 Sep;134(5):1179–1195. [PMC free article] [PubMed]
  • Valge-Archer VE, Osada H, Warren AJ, Forster A, Li J, Baer R, Rabbitts TH. The LIM protein RBTN2 and the basic helix-loop-helix protein TAL1 are present in a complex in erythroid cells. Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8617–8621. [PMC free article] [PubMed]
  • Wadman I, Li J, Bash RO, Forster A, Osada H, Rabbitts TH, Baer R. Specific in vivo association between the bHLH and LIM proteins implicated in human T cell leukemia. EMBO J. 1994 Oct 17;13(20):4831–4839. [PMC free article] [PubMed]
  • Warren AJ, Colledge WH, Carlton MB, Evans MJ, Smith AJ, Rabbitts TH. The oncogenic cysteine-rich LIM domain protein rbtn2 is essential for erythroid development. Cell. 1994 Jul 15;78(1):45–57. [PubMed]
  • Weiskirchen R, Pino JD, Macalma T, Bister K, Beckerle MC. The cysteine-rich protein family of highly related LIM domain proteins. J Biol Chem. 1995 Dec 1;270(48):28946–28954. [PubMed]
  • Wu RY, Gill GN. LIM domain recognition of a tyrosine-containing tight turn. J Biol Chem. 1994 Oct 7;269(40):25085–25090. [PubMed]
  • Yang HY, Evans T. Distinct roles for the two cGATA-1 finger domains. Mol Cell Biol. 1992 Oct;12(10):4562–4570. [PMC free article] [PubMed]

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