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Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition.

An YJ, Ahn BE, Han AR, Kim HM, Chung KM, Shin JH, Cho YB, Roe JH, Cha SS - Nucleic Acids Res. (2009)

Bottom Line: This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif.The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns.Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.

View Article: PubMed Central - PubMed

Affiliation: Marine and Extreme Genome Research Center, Korea Ocean Research & Development Institute, Ansan 426-744, Republic of Korea.

ABSTRACT
Nur, a member of the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in Streptomyces coelicolor. Here we report the 2.4-A resolution crystal structure of Nur. It contains a unique nickel-specific metal site in addition to a nonspecific common metal site. The identification of the 6-5-6 motif of the Nur recognition box and a Nur/DNA complex model reveals that Nur mainly interacts with terminal bases of the palindrome on complex formation. This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif. The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns. Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.

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The proposed Nur box sequence and a model for Nur/DNA complex. (A) Palindromic sequences conserved within Nur-binding sites. The primary DNase I- protected regions in sodF, sodF2, nikA and nikM promoters by Nur binding (Supplementary Figure S1) were aligned, and a conserved palindromic pattern was proposed for Nur-binding consensus. (B) The front view of a Nur/DNA complex model. Nickel ions at Ni-site are shown by red spheres. The S1–S2 sheets are colored in yellow for emphasis. The 17-bp Nur box DNA in sodF promoter and DNA-contacting residues (Tyr56, Arg57 and Asp37) are shown in violet and blue sticks, respectively. Recognition helices (H4) are labeled. A black rectangle highlights the location of S1–S2 sheets on top of the central minor groove [see also (D)]. (C) The contacting face of the Nur box DNA in the Nur/DNA complex model. A green ellipsoid indicates the central minor groove. (D) The top view of the Nur/DNA complex model. For clarity, Nur is represented by a green surface with recognition helices and the S1–S2 sheets shown by ribbon drawing. DNA is shown in sticks covered with violet surface. The orange arrows indicate the deduced induced fit on complex formation. Tyr56, Arg57 and Asp37 are shown in blue sticks. Recognition helices (H4) are labeled. (E) DNA-binding activity of Nur variants with mutations of residues contacting DNA. Nur variants with mutations for R57, Y56 and D37 were examined as in Figure 1E.
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Figure 3: The proposed Nur box sequence and a model for Nur/DNA complex. (A) Palindromic sequences conserved within Nur-binding sites. The primary DNase I- protected regions in sodF, sodF2, nikA and nikM promoters by Nur binding (Supplementary Figure S1) were aligned, and a conserved palindromic pattern was proposed for Nur-binding consensus. (B) The front view of a Nur/DNA complex model. Nickel ions at Ni-site are shown by red spheres. The S1–S2 sheets are colored in yellow for emphasis. The 17-bp Nur box DNA in sodF promoter and DNA-contacting residues (Tyr56, Arg57 and Asp37) are shown in violet and blue sticks, respectively. Recognition helices (H4) are labeled. A black rectangle highlights the location of S1–S2 sheets on top of the central minor groove [see also (D)]. (C) The contacting face of the Nur box DNA in the Nur/DNA complex model. A green ellipsoid indicates the central minor groove. (D) The top view of the Nur/DNA complex model. For clarity, Nur is represented by a green surface with recognition helices and the S1–S2 sheets shown by ribbon drawing. DNA is shown in sticks covered with violet surface. The orange arrows indicate the deduced induced fit on complex formation. Tyr56, Arg57 and Asp37 are shown in blue sticks. Recognition helices (H4) are labeled. (E) DNA-binding activity of Nur variants with mutations of residues contacting DNA. Nur variants with mutations for R57, Y56 and D37 were examined as in Figure 1E.

Mentions: To elucidate the regulatory mechanism of Nur at the transcription level, it is essential to characterize the Nur–DNA recognition mechanism. For this purpose, the consensus DNA sequences were searched among Nur-binding promoter regions. In addition to previously identified genes (sodF, sodF2 and nikABCDE) (5), a new type of nickel transporter (nikMNOQ) has been suggested in S. coelicolor (23) and we determined that Nur also binds to nikM promoter DNA in a nickel-dependent manner (see Supplementary Figure S1). The Nur-binding sites in each promoter region were analyzed by DNase I footprinting (Supplementary Figure S1), and the nucleotide sequences of primary protected regions were aligned. A consensus Nur box emerged with a palindromic structure of six residues with 5-bp spacing (tTGCaa-N5-ttGCAA). The 6-5-6 motif implies that five nonconserved bases in the middle of the motif may contribute little to interactions with Nur (Figure 3A).Figure 3.


Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition.

An YJ, Ahn BE, Han AR, Kim HM, Chung KM, Shin JH, Cho YB, Roe JH, Cha SS - Nucleic Acids Res. (2009)

The proposed Nur box sequence and a model for Nur/DNA complex. (A) Palindromic sequences conserved within Nur-binding sites. The primary DNase I- protected regions in sodF, sodF2, nikA and nikM promoters by Nur binding (Supplementary Figure S1) were aligned, and a conserved palindromic pattern was proposed for Nur-binding consensus. (B) The front view of a Nur/DNA complex model. Nickel ions at Ni-site are shown by red spheres. The S1–S2 sheets are colored in yellow for emphasis. The 17-bp Nur box DNA in sodF promoter and DNA-contacting residues (Tyr56, Arg57 and Asp37) are shown in violet and blue sticks, respectively. Recognition helices (H4) are labeled. A black rectangle highlights the location of S1–S2 sheets on top of the central minor groove [see also (D)]. (C) The contacting face of the Nur box DNA in the Nur/DNA complex model. A green ellipsoid indicates the central minor groove. (D) The top view of the Nur/DNA complex model. For clarity, Nur is represented by a green surface with recognition helices and the S1–S2 sheets shown by ribbon drawing. DNA is shown in sticks covered with violet surface. The orange arrows indicate the deduced induced fit on complex formation. Tyr56, Arg57 and Asp37 are shown in blue sticks. Recognition helices (H4) are labeled. (E) DNA-binding activity of Nur variants with mutations of residues contacting DNA. Nur variants with mutations for R57, Y56 and D37 were examined as in Figure 1E.
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Figure 3: The proposed Nur box sequence and a model for Nur/DNA complex. (A) Palindromic sequences conserved within Nur-binding sites. The primary DNase I- protected regions in sodF, sodF2, nikA and nikM promoters by Nur binding (Supplementary Figure S1) were aligned, and a conserved palindromic pattern was proposed for Nur-binding consensus. (B) The front view of a Nur/DNA complex model. Nickel ions at Ni-site are shown by red spheres. The S1–S2 sheets are colored in yellow for emphasis. The 17-bp Nur box DNA in sodF promoter and DNA-contacting residues (Tyr56, Arg57 and Asp37) are shown in violet and blue sticks, respectively. Recognition helices (H4) are labeled. A black rectangle highlights the location of S1–S2 sheets on top of the central minor groove [see also (D)]. (C) The contacting face of the Nur box DNA in the Nur/DNA complex model. A green ellipsoid indicates the central minor groove. (D) The top view of the Nur/DNA complex model. For clarity, Nur is represented by a green surface with recognition helices and the S1–S2 sheets shown by ribbon drawing. DNA is shown in sticks covered with violet surface. The orange arrows indicate the deduced induced fit on complex formation. Tyr56, Arg57 and Asp37 are shown in blue sticks. Recognition helices (H4) are labeled. (E) DNA-binding activity of Nur variants with mutations of residues contacting DNA. Nur variants with mutations for R57, Y56 and D37 were examined as in Figure 1E.
Mentions: To elucidate the regulatory mechanism of Nur at the transcription level, it is essential to characterize the Nur–DNA recognition mechanism. For this purpose, the consensus DNA sequences were searched among Nur-binding promoter regions. In addition to previously identified genes (sodF, sodF2 and nikABCDE) (5), a new type of nickel transporter (nikMNOQ) has been suggested in S. coelicolor (23) and we determined that Nur also binds to nikM promoter DNA in a nickel-dependent manner (see Supplementary Figure S1). The Nur-binding sites in each promoter region were analyzed by DNase I footprinting (Supplementary Figure S1), and the nucleotide sequences of primary protected regions were aligned. A consensus Nur box emerged with a palindromic structure of six residues with 5-bp spacing (tTGCaa-N5-ttGCAA). The 6-5-6 motif implies that five nonconserved bases in the middle of the motif may contribute little to interactions with Nur (Figure 3A).Figure 3.

Bottom Line: This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif.The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns.Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.

View Article: PubMed Central - PubMed

Affiliation: Marine and Extreme Genome Research Center, Korea Ocean Research & Development Institute, Ansan 426-744, Republic of Korea.

ABSTRACT
Nur, a member of the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in Streptomyces coelicolor. Here we report the 2.4-A resolution crystal structure of Nur. It contains a unique nickel-specific metal site in addition to a nonspecific common metal site. The identification of the 6-5-6 motif of the Nur recognition box and a Nur/DNA complex model reveals that Nur mainly interacts with terminal bases of the palindrome on complex formation. This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif. The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns. Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.

Show MeSH
Related in: MedlinePlus