Zinc-binding domains

The general topology of rubredoxins is also observed in the general zinc-ribbon motif in RNA polymerases or in transcription factors (59). The first published zinc-ribbon structure was that of the nucleic-acid binding domain of human transcriptional elongation factor TFIIS (PDB file ITFI) 40). These zinc binding domains and rubredoxins... 

ZnFZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein E(MFP) 2(2) 11(12) ... 

Tab. 4.1. Alternative zinc-binding domains in RING proteins.

Capili, a. D., et al., Structure of the C-terminal RING Finger from a RING-IBR-RING/TRIAD Motif Reveals a Novel Zinc-binding Domain Distinct from a RING. / Mol Biol,... 

Boddy, M. N., P. S. Freemont, and K. L Borden, The p53-associated protein MDM2 contains a newly characterized zinc-binding domain called the RING finger. Trends Biochem Sci, 1994, 19(5), 198-9. 

WOETHINGTON, M. T., et al.. Metal binding properties and secondary structure of the zinc-binding domain of Nup475. Proc Natl Acad Sci USA, 1996, 93(24), 13754-9. 

W. A. Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J. 

The class III deacetylases, named sirtuins, are structurally and functionally different from other HDACs. In contrast to the zinc-dependent deacetylation of classic HDACs, sirtuins depend on NAD" to carry out catalytic reactions. A variety of sirtuin crystal structures have been published over the past few years. The structures of human Sirt2 and SirtS as well as several bacterial Sir2 proteins could be derived, whereas no 3D structure is available for Sirtl and the other subtypes [69]. All solved sirtuin structures contain a conserved 270-amino-acid catalytic domain with variable N- and C-termini. The structure of the catalytic domain consists of a large classic Rossmann fold and a small zinc binding domain. The interface between the large and the small subdomain is commonly subdivided into A, B and C pockets. This division is based on the interaction of adenine (A), ribose (B) and nicotinamide (C) which are parts of the NAD" cofactor. (Figure 3.5) Whereas the interaction of adenine and... 

Fig. 43. The structure of the CyssHis zinc-binding domain derived from the gag protein p55 from human immunodeficiency virus, as determined by solution NMR methods. [Reprinted with permission from Summers, M. F., South, T. L., Kim, B., Hare, D. R. (1990) Biochemistry 29, 329-340. Copyright 1990 American Chemical Society.]...

Miller, J. (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J 4 1609-1614. 

TPR (Tetratrico peptide repeat)247,275,276 ZBD (Zinc-binding domains) Zinc finger (Fig. 5-37)277 Others277-280 ... 

Lichtarge, O., Yamamoto, K. R., Cohen, F. E. Identification of functional surfaces of the zinc binding domains of intracellular receptors. J. Mol. Biol., 1997, 274, 325-337. 

Metal-dependent Structure and Self Association of the RAGl Zinc-Binding Domain... 

The circular dichroism (CD) spectrum of the fully zinc-coordinated (native) ZDD as well as of an apo form is shown in Figure 2A. Removal of all zinc ions to produce the apo form of the domain results in extensive loss of ordered secondary structure as judged by the reduction of molar ellipticity in the CD spectrum. As in other structural zinc-binding domains, we conclude that the free energy associated with the coordination of metal ions is necessary for correct folding of ZDD. 

Payne, J.C., M.L. Horst and H.A. Godwin. Lead fingers Pb2+ binding to structural zinc-binding domains determined directly by monitoring lead-thiolate charge-transfer bands. J. Am. Chem. Soc. 121 6850-6855, 1999. 

Bottomley MJ et al (2008) Structural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain. J Biol Chem 283(39) 26694-26704... 

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