PDBsum entry 1m4z

Gene regulation

PDB id

1m4z

Contents

			Protein chains

					203 a.a.

			Metals

					_MN ×3

			Waters ×266

References listed in PDB file

Key reference

Title

Structure and function of the bah-Containing domain of orc1p in epigenetic silencing.

Authors

Z.Zhang, M.K.Hayashi, O.Merkel, B.Stillman, R.M.Xu.

Ref.

EMBO J, 2002, 21, 4600-4611. [DOI no: 10.1093/emboj/cdf468]

PubMed id

12198162

Abstract

The N-terminal domain of the largest subunit of the Saccharomyces cerevisiae origin recognition complex (Orc1p) functions in transcriptional silencing and contains a bromo-adjacent homology (BAH) domain found in some chromatin-associated proteins including Sir3p. The 2.2 A crystal structure of the N-terminal domain of Orc1p revealed a BAH core and a non-conserved helical sub-domain. Mutational analyses demonstrated that the helical sub-domain was necessary and sufficient to bind Sir1p, and critical for targeting Sir1p primarily to the cis-acting E silencers at the HMR and HML silent chromatin domains. In the absence of the BAH domain, approximately 14-20% of cells in a population were silenced at the HML locus. Moreover, the distributions of the Sir2p, Sir3p and Sir4p proteins, while normal, were at levels lower than found in wild-type cells. Thus, in the absence of the Orc1p BAH domain, HML resembled silencing of genes adjacent to telomeres. These data are consistent with the view that the Orc1p-Sir1p interaction at the E silencers ensures stable inheritance of pre-established Sir2p, Sir3p and Sir4p complexes at the silent mating type loci.



	Figure 1. Figure 1 The structure of the N-terminal domain of Orc1p. (A) Structure-guided sequence alignment of the N-terminal region of S.cerevisiae Orc1p (yOrc1) with the BAH domain-containing region of Sir3p (ySir3), human Orc1p (hOrc1), DNA-(cytosine-5)-methyltransferase 1 (Dnmt1), the human metastasis-associated protein 1 (Mta1) and S.cerevisiae Rsc1. The amino acids shown in white letters on a black background are invariant; white letters on a gray background indicate that similar amino acids are found in at least five proteins. Amino acids similar among yOrc1, ySir3 and hOrc1 are highlighted in cyan, and amino acids identical between yOrc1 and ySir3 are in blue rectangles. Green highlights the position of SIR3 mutants suppressing histone H4 and Rap1 mutations (Johnson et al., 1990; Liu and Lustig, 1996). Residues highlighted in yellow and red are class I and class II Sir3p mutants, respectively, which enhance the sir1 mating-defective phenotype (Stone et al., 2000). Secondary structural elements are colored as in (C) and shown above the sequences. Every 10 aa are indicated with a + sign. Residues shown in red were removed in the orc1m1 and orc1m2 mutants of yOrc1. In the orc1m1 mutant, the amino acids shown in red were replaced by the amino acids from hOrc1, also shown in red. (B) The crystal structure is shown in a ribbon representation. (C) Topology diagram showing the fold of the structure. The core of the structure consists mainly of -strands and is colored cyan. The H domain is shown in magenta, and N- and C-terminal helices are shown in red. -strands are numbered consecutively and -helices are labeled alphabetically from the N- to the C-terminus.		Figure 7. Figure 7 Grasp surface representation of the structure. (A) The location of Sir3p mutants mapped onto the Orc1pN235 structure (with the Orc1p amino acids labeled). As in Figure 1A, green indicates the position of mutants that suppress histone H4 mutations. Red indicates class II and yellow indicates class I sir3 mutants that enhance the sir1mutant defect (Stone et al., 2000). (B) Electrostatic potential distribution on the Orc1pN235 surface. Red indicates negative (-15 K[B]T), white indicates neutral (0 K[B]T) and blue indicates positive (+15 K K[B]T) charges, where K[B] is the Boltzmann constant and T is the temperature.

PROCHECK

	Headers