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Two high-mobility group box domains act together to underwind and kink DNA.

Sánchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill ME, Campos JL - Acta Crystallogr. D Biol. Crystallogr. (2015)

Bottom Line: Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å.Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA.This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

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Affiliation: Departament d'Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain.

ABSTRACT
High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1-DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

No MeSH data available.


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The kinked DNA structure. (a) DNA–box A contacts (NUCPLOT). Hydrogen bonds are shown as solid lines and nonbound contacts are shown as dashed lines. (b) Close-up views of the protein–DNA purine base interactions. Hydrogen bonds from residues Phe37 and Ser41 to base pairs A7 and G6 and a water-mediated hydrogen bond from Ser13 to A9 are shown in the upper and lower diagrams, respectively. (c) Comparison of DNA parameters for HMG-box intercalation sites. The roll and twist angles for box A in this structure were obtained with 3DNA, and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al., 1999 ▸), 2gzk (box B; Stott et al., 2006 ▸), 1qrv (HMGD; Murphy et al., 1999 ▸), 1j5n (NHP6A; Masse et al., 2002 ▸) and 3tmm (TFAM; Ngo et al., 2011 ▸) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2). (d) Superimposition of box A kinked DNA (orange) with cisplatin-modified DNA (grey).
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fig3: The kinked DNA structure. (a) DNA–box A contacts (NUCPLOT). Hydrogen bonds are shown as solid lines and nonbound contacts are shown as dashed lines. (b) Close-up views of the protein–DNA purine base interactions. Hydrogen bonds from residues Phe37 and Ser41 to base pairs A7 and G6 and a water-mediated hydrogen bond from Ser13 to A9 are shown in the upper and lower diagrams, respectively. (c) Comparison of DNA parameters for HMG-box intercalation sites. The roll and twist angles for box A in this structure were obtained with 3DNA, and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al., 1999 ▸), 2gzk (box B; Stott et al., 2006 ▸), 1qrv (HMGD; Murphy et al., 1999 ▸), 1j5n (NHP6A; Masse et al., 2002 ▸) and 3tmm (TFAM; Ngo et al., 2011 ▸) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2). (d) Superimposition of box A kinked DNA (orange) with cisplatin-modified DNA (grey).

Mentions: The two box A domains bind in an approximately symmetric manner about the dyad axis of the palindromic DNA decamer, with water-mediated interactions between the domains (Supplementary Fig. S4). Molecule A contacts one half of the duplex, from A1/T20 to C5/G16, and molecule B contacts the other half, from G6/C15 to T10/A11 (Figs. 2 ▸a, 2 ▸b and 3 ▸a). The two domains enclose the DNA (Figs. 2 ▸a and 2 ▸c), unwinding and bending it by approximately 85°, with intercalation of the two Phe37 residues at the central CG base pair (Figs. 2 ▸b and 2 ▸d and Supplementary Table S1). This tail-to-tail mode of binding places both Phe37 side chains in a cleft created in the DNA minor groove (Figs. 2 ▸b and 2 ▸d), producing a prominent kink in the DNA towards the major groove. The two phenyl rings of Phe37 are parallel to each other at 3.5 Å, a distance indicative of π-stacking. These features contrast with the other multi-domain HMG-box–DNA structures: HMGD domains interact in a head-to-head orientation (Murphy et al., 1999 ▸), SRY.B domains bind in a head-to-head fashion with the two 2° intercalation sites separated by 16 bp (Stott et al., 2006 ▸) and TFAM HMG domains bind tail to tail but the two 2° intercalation sites are separated by 11 bp (Ngo et al., 2011 ▸, 2014 ▸; Rubio-Cosials et al., 2011 ▸). Thus, this collaborative binding mode, whereby the 2° intercalation residues of two HMG box A domains act in the same base step, has not previously been observed.


Two high-mobility group box domains act together to underwind and kink DNA.

Sánchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill ME, Campos JL - Acta Crystallogr. D Biol. Crystallogr. (2015)

The kinked DNA structure. (a) DNA–box A contacts (NUCPLOT). Hydrogen bonds are shown as solid lines and nonbound contacts are shown as dashed lines. (b) Close-up views of the protein–DNA purine base interactions. Hydrogen bonds from residues Phe37 and Ser41 to base pairs A7 and G6 and a water-mediated hydrogen bond from Ser13 to A9 are shown in the upper and lower diagrams, respectively. (c) Comparison of DNA parameters for HMG-box intercalation sites. The roll and twist angles for box A in this structure were obtained with 3DNA, and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al., 1999 ▸), 2gzk (box B; Stott et al., 2006 ▸), 1qrv (HMGD; Murphy et al., 1999 ▸), 1j5n (NHP6A; Masse et al., 2002 ▸) and 3tmm (TFAM; Ngo et al., 2011 ▸) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2). (d) Superimposition of box A kinked DNA (orange) with cisplatin-modified DNA (grey).
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fig3: The kinked DNA structure. (a) DNA–box A contacts (NUCPLOT). Hydrogen bonds are shown as solid lines and nonbound contacts are shown as dashed lines. (b) Close-up views of the protein–DNA purine base interactions. Hydrogen bonds from residues Phe37 and Ser41 to base pairs A7 and G6 and a water-mediated hydrogen bond from Ser13 to A9 are shown in the upper and lower diagrams, respectively. (c) Comparison of DNA parameters for HMG-box intercalation sites. The roll and twist angles for box A in this structure were obtained with 3DNA, and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al., 1999 ▸), 2gzk (box B; Stott et al., 2006 ▸), 1qrv (HMGD; Murphy et al., 1999 ▸), 1j5n (NHP6A; Masse et al., 2002 ▸) and 3tmm (TFAM; Ngo et al., 2011 ▸) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2). (d) Superimposition of box A kinked DNA (orange) with cisplatin-modified DNA (grey).
Mentions: The two box A domains bind in an approximately symmetric manner about the dyad axis of the palindromic DNA decamer, with water-mediated interactions between the domains (Supplementary Fig. S4). Molecule A contacts one half of the duplex, from A1/T20 to C5/G16, and molecule B contacts the other half, from G6/C15 to T10/A11 (Figs. 2 ▸a, 2 ▸b and 3 ▸a). The two domains enclose the DNA (Figs. 2 ▸a and 2 ▸c), unwinding and bending it by approximately 85°, with intercalation of the two Phe37 residues at the central CG base pair (Figs. 2 ▸b and 2 ▸d and Supplementary Table S1). This tail-to-tail mode of binding places both Phe37 side chains in a cleft created in the DNA minor groove (Figs. 2 ▸b and 2 ▸d), producing a prominent kink in the DNA towards the major groove. The two phenyl rings of Phe37 are parallel to each other at 3.5 Å, a distance indicative of π-stacking. These features contrast with the other multi-domain HMG-box–DNA structures: HMGD domains interact in a head-to-head orientation (Murphy et al., 1999 ▸), SRY.B domains bind in a head-to-head fashion with the two 2° intercalation sites separated by 16 bp (Stott et al., 2006 ▸) and TFAM HMG domains bind tail to tail but the two 2° intercalation sites are separated by 11 bp (Ngo et al., 2011 ▸, 2014 ▸; Rubio-Cosials et al., 2011 ▸). Thus, this collaborative binding mode, whereby the 2° intercalation residues of two HMG box A domains act in the same base step, has not previously been observed.

Bottom Line: Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å.Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA.This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament d'Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain.

ABSTRACT
High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1-DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

No MeSH data available.


Related in: MedlinePlus