Y2H35 a strong IKK binding protein

Details Y2H35 a strong IKK binding protein Y2H35 a strong IKK binding protein

1998-11-16

2001-04-10

Pronty, Rebecca E. (Department: 1652)

Chemistry: molecular biology and microbiology

Micro-organism, tissue cell culture or enzyme using process...

Recombinant dna technique included in method of making a...

C435S320100, C435S325000, C435S252300, C435S006120, C536S023100, C536S023500

Reexamination Certificate

active

06214582

ABSTRACT:

BACKGROUND OF THE INVENTION
The NF-&kgr;B family of transcription factors are involved in the regulation of a wide variety of cellular responses. These transcription factors mediate extracellular signals that induce expression of genes involved in such diverse processes as cell division, inflammation, and apoptosis. See, for example, Baldwin, Annu. Rev. Immunol. 12, 141-179 (1996); Beg and Baltimore, Science 274, 782-274 (1996); Gilmore et al., Oncogene 13, 1267-1378 (1996); Mayo, et al, Science 278, 1812-1815 (1997); and Van Antwerp et al., Science 274, 787-789 (1996); Ashkenazi and Dixit, Science 281, 1305-1308 (1998).
NF-&kgr;B is anchored in the cytoplasm of most non-stimulated cells by a non-covalent interaction with one of several inhibitory proteins known as I&kgr;Bs. See for example, Baeuerle and Baltimore, Science 242, 540-546 (1988). Cellular stimuli associated with immune and inflammatory responses, for example inflammatory cytokines such as tumor necrosis factor &agr; (TNF&agr;) or interleukin-1 (IL-1), activate kinases, which in turn activate NF-&kgr;B by phosphorylating I&kgr;Bs. The kinases that phosphorylate I&kgr;Bs are called I&kgr;B kinases (IKKs).
Phosphorylation marks the I&kgr;Bs for ubiquitination and proteosome mediated degradation. The degradation and dissociation, of I&kgr;Bs from NF-&kgr;B unmasks the NF-&kgr;B nuclear localization signal, and facilitates the nuclear translocation of active NF-&kgr;B to the nucleus, thereby upregulating NF-&kgr;B responsive target genes. See, for example, Baeuerle and Henkel, Annu. Rev. Immunol. 12, 141-179 (1994); Baldwin, Annu.Rev. Immunol. 14, 649-683 (1996); Siebenlist et al., Annu.Rev.Cell Biol. 12, 405-455 (1994); and Verma et al, Genes Dev. 9, 2723-2735 (1995). Thus, this phosphorylation of I&kgr;Bs is a key regulatory step for NF-&kgr;B mediated processes.
The determination and characterization of kinases that directly phosphorylate I&kgr;Bs are instrumental in the delineation of signaling pathways involving NF-&kgr;B activation. Recently, an I&kgr;B kinase, designated IKK&agr; but also referred to as CHUK (conserved helix-loop-helix ubiquitous kinase), was identified in a yeast-two-hybrid screen with NIK as bait. Regnier et al., Cell 90, 373-383 (1997). IKK&agr; was determined to be responsible for the major I&kgr;B kinase activity induced by TNF stimulation of HeLa cells. DiDonato et al., Nature 388, 548-554 (1997). The identification of IKK&agr; as a cytoplasmic kinase which phosphorylates I&kgr;B family members at their physiologically relevant sites and targets them for proteosome-mediated degradation was a major breakthrough.
The IKK&agr; gene encodes a 745 amino-acid polypeptide (having a molecular mass of approximately 85 kDa). Murine and human IKK&agr; cDNA clones were found to be almost identical. Connelly and Marcu, Cellular and Molecular Biology Research 41, 537-549 (1995).
Another kinase, termed IKK&bgr;, homologous to IKK&agr;, has also been reported. Stancovski and Baltimore, Cell 91, 299-302 (1997); Woronicz et al., Science 278, 866-869 (1997); and Zandi et al., Cell 91, 243-252 (1997). IKK&agr; and IKK&bgr; have 52% overall similarity to each other and 65% identity in the kinase domain. Zandi et al., Cell 91, 243-252 (1997). An I&kgr;B kinase termed T2K has also been described in U.S. Pat. No. 5,776,717 to Cao.
The known I&kgr;B protein kinases generally phosphorylate I&kgr;Bs at specific serine residues. For example, they specifically phosphorylate serines 32 and 36 of I&kgr;B&agr;. Phosphorylation of both sites is required to efficiently target I&kgr;B&agr; for destruction in vivo. Moreover, activation of IKK&agr; and IKK&bgr; occurs in response to NF-&kgr;B activating agents and mutant IKK&agr; and IKK&bgr; that are catalytically inactive block NF-&kgr;B stimulation by cytokines. These results highlight the important role played by I&kgr;B protein kinases in NF-&kgr;B activation processes. See Stancovski and Baltimore, Cell 91, 299-302 (1997) for a recent discussion of I&kgr;B kinases.
IKK&agr; and IKK&bgr; have structural motifs characteristic of the IKK kinases. This includes an amino terminal serine-threonine kinase domain separated from a carboxyl proximal helix-loop-helix (H-L-H) domain by a leucine zipper domain. These structural characteristics are unlike other kinases, and the domains are thought to be involved in protein-protein interactions.
Numerous proteins are involved in the signaling pathways that lead to immune, inflammatory, and apoptotic responses. A complete elucidation of these processes requires the identification of additional proteins that are involved and a determination of the protein interactions.
The discovery of additional proteins involved in these processes is important for controlling immune, apoptotic, and inflammatory processes. Thus, there is a great need for the identification and characterizion of additional proteins involved in IKK mediated cellular processes.
SUMMARY OF THE INVENTION
The present invention provides an isolated IKK binding protein, designated Y2H35, comprising the amino acid sequence set forth in SEQ ID NO:1 and functional equivalents. Also included are isolated nucleic acid molecules that encode Y2H35. Methods of making Y2H35 comprising expressing nucleic acid molecules encoding the protein are also provided. Antibodies directed to Y2H35 are also included in the invention.
DETAILED DESCRIPTION OF THE INVENTION
The invention is directed to an IKK binding protein, designated Y2H35, and its functional equivalents. Y2H35 will hereinafter refer to the protein defined by SEQ ID NO:1, which is found in humans.
In this specification, functional equivalents are proteins or fragments that are substantially homologous to SEQ ID NO:1 and that specifically bind to an IKK protein, such as IKK&agr; or IKK&bgr;. The term IKK is used herein to refer to all kinases that phosphorylate any I&kgr;B and that have helix-loop-helix and leucine zipper domains. Y2H35 and its functional equivalents bind to the region of the IKK proteins made up of the contiguous helix-loop-helix and leucine zipper domains.
In order to determine whether the sequence of a first protein, or fragment thereof, is substantially homologous to the sequence of a second protein, such as Y2H35, or fragment thereof, the sequences are first aligned so as to optimize the percent of amino acid residues that are identical, or that are identical or equivalent, at corresponding positions. Gaps may be introduced in the sequences, if necessary, to achieve optimization.
Amino acids generally considered to be equivalent are indicated below in separate rows (a) through (e):
(a) Ala (A), Ser (S), Thr (T), Pro (P), Gly (G)
(b) Asn (N), Asp (D), Glu (E), Gln (Q)
(c) His (H), Arg (R), Lys (K)
(d) Met (M), Leu (L), Ile (I), Val (V)
(e) Phe (F), Tyr (Y), Trp (W)
The amino acid sequences of highly homologous proteins can usually be aligned by visual inspection. If visual inspection is insufficient, the proteins are aligned in accordance with any of the methods described by George, D. G. et al, in
Macromolecular Sequencing and Synthesis, Selected Methods and Applications,
pages 127-149, Alan R. Liss, Inc. (1988), such as the formula described at page 137 using a match score of 1, a mismatch score of 0, and a gap penalty of −1.
In a first embodiment, the sequence of a protein or fragment thereof is considered substantially homologous to the sequence of Y2H35 or a fragment thereof if the amino acid sequences, after alignment, are at least about 25% identical, preferably at least about 35% identical, more preferably at least about 50% identical, even more preferably at least about 65% identical, still more preferably at least about 75% identical, most preferably at least about 85% identical, and, ideally at least about 95% identical.
In a second embodiment, the sequence of a protein or fragment thereof is considered substantially homologous to the sequence of Y2H35 or a fragment thereof if the amino acid sequences, after alignment, are at least about 50% identical or equivalent, preferably at least about

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