The PR/SET domain in PRDM4 is preceded by a zinc knuckle.

PR proteins play key roles in various aspects of cell differentiation and organismal development, and, when dysregulated, are involved in carcinogenesis.1–6 The defining feature of PR proteins is a conserved sequence termed the PR (PRDI-BF1 and RIZ1 homology) domain,7 which is almost always accompanied by an array of C2H2-like zinc fingers. Other sequences that are present in PR proteins show limited conservation and contain virtually no discernible motifs. The PR domain is a significantly diverged variant of a SET domain,8 a motif with protein (often histone) lysine N-methyltransferase activity.9 However, amino acid sequence identity between PR domains and canonical SET domains is typically less than 25%, and a number of residues that are conserved in canonical SET domains and believed to be important for enzymatic activity are not conserved in PR domains.1 Hence, it is not surprising that from the 17 PR proteins identified in humans, only two (PRDM2/RIZ110 and PRDM9/meisetz4) have been demonstrated to have intrinsic histone lysine methyltransferase activity that is detectable in assays using radioactive substrate. Efforts to detect intrinsic methyltransferase activity of other PR proteins have been unsuccessful,11–13 and hence, it remains to be determined how these proteins carry out their regulatory functions. Several PR proteins have been shown to interact with other transcriptional factors,7,11–15 and hence, instead of modifying chromatin themselves, they may mediate protein-protein interactions and recruit other proteins (including chromatin modifying enzymes) to chromatin. PRDM4 (Schwann cell factor 1, SC-1) is a member of the PR protein family.16 It is a transcriptional regulator that has been implied in transduction of nerve growth factor signals via the p75 neurotrophin receptor and in cell growth arrest15,17 and is expressed in a variety of tissues including the central and peripheral nervous systems.16,18 Interestingly, we noticed that the PR domain in PRDM4 is preceded by a short motif that is also present in several other PR proteins including human PRDM6 (PRISM),13,19 PRDM7,20 PRDM9 (meisetz),4,21–23 PRDM10 (tristanin),24,25 PRDM11, and PRDM1526 [Fig. 1(A,B)]. The conservation of cysteine and histidine residues suggested that this 20 amino acid motif binds zinc, and hence, we refer to it as the ‘‘PR zinc knuckle’’ to distinguish it from the longer ( 30 amino acid) C2H2-like zinc fingers that are located C-terminally of the PR domain. In addition to identifying this motif, we demonstrate in this report that the PR zinc knuckle indeed coordinates zinc and we present its 3-dimensional structure determined by NMR spectroscopy.