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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.

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

HMG-box sequence comparison. Sequence alignment of non-sequence-specific HMG-box proteins: HMGB1 (rat; rHMGB1-A, box A; rHMGB1-B, box B), HMGD (Drosophila), NHP6A (S. cerevisiae), sequence-specific/non-sequence-specific TFAM (human mitochondria; TFAM-HMG1, box A; TFAM-HMG2, box B) and sequence-specific SRY (human) and LEF1 (mouse). The three α-helices of the HMG box are shown above the alignment. Arrows indicate the 1° and 2° intercalating residues. Conserved residues (Clustal Omega alignment) are highlighted in gray, where an asterisk (*) indicates complete conservation, a colon (:) indicates conservation between groups with strongly similar properties and a dot (.) indicates conservation between groups with weakly similar properties.
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fig1: HMG-box sequence comparison. Sequence alignment of non-sequence-specific HMG-box proteins: HMGB1 (rat; rHMGB1-A, box A; rHMGB1-B, box B), HMGD (Drosophila), NHP6A (S. cerevisiae), sequence-specific/non-sequence-specific TFAM (human mitochondria; TFAM-HMG1, box A; TFAM-HMG2, box B) and sequence-specific SRY (human) and LEF1 (mouse). The three α-helices of the HMG box are shown above the alignment. Arrows indicate the 1° and 2° intercalating residues. Conserved residues (Clustal Omega alignment) are highlighted in gray, where an asterisk (*) indicates complete conservation, a colon (:) indicates conservation between groups with strongly similar properties and a dot (.) indicates conservation between groups with weakly similar properties.

Mentions: A hallmark of HMGB proteins is their ability to recognize the minor groove of pre-bent, distorted or linear DNA, bending linear DNA between 70 and 180° towards the major groove (Dragan et al., 2003 ▸, 2004 ▸; Werner et al., 1995 ▸). The HMGB1 domains are unequal in these properties: box A recognizes both pre-bent (Teo, Grasser & Thomas, 1995 ▸) and linear DNA more tightly than box B (Müller et al., 2001 ▸), but box B binds to mini-circles (Webb et al., 2001 ▸) and bends linear DNA to a greater extent than box A (Paull et al., 1993 ▸; Teo, Grasser & Thomas, 1995 ▸). This dramatic distortion of DNA is dependent on both shape complementarity and DNA intercalation of two apolar residues (Churchill et al., 2010 ▸; Klass et al., 2003 ▸; Murphy & Churchill, 2000 ▸; Roemer et al., 2008 ▸). The primary intercalation residue is in helix I (1° in Fig. 1 ▸) and the second intercalation wedge (2° in Fig. 1 ▸) is at the start of helix II. HMGB1 box A is an exception because Ala16 at the 1° site cannot intercalate DNA but Phe37 at the 2° site can, and this is thought to be responsible for the superior ability of box A to recognize pre-bent DNA (reviewed by Štros, 2010 ▸). Indeed, the crystal structure of box A bound to cisplatin intrastrand GG cross-linked DNA showed Phe37 lodged into the cisplatin-induced kink, although the DNA itself was relatively undistorted compared with the free cisplatin-modified DNA (Ohndorf et al., 1999 ▸). However, how box A recognizes natural, unmodified DNA remains unknown.


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)

HMG-box sequence comparison. Sequence alignment of non-sequence-specific HMG-box proteins: HMGB1 (rat; rHMGB1-A, box A; rHMGB1-B, box B), HMGD (Drosophila), NHP6A (S. cerevisiae), sequence-specific/non-sequence-specific TFAM (human mitochondria; TFAM-HMG1, box A; TFAM-HMG2, box B) and sequence-specific SRY (human) and LEF1 (mouse). The three α-helices of the HMG box are shown above the alignment. Arrows indicate the 1° and 2° intercalating residues. Conserved residues (Clustal Omega alignment) are highlighted in gray, where an asterisk (*) indicates complete conservation, a colon (:) indicates conservation between groups with strongly similar properties and a dot (.) indicates conservation between groups with weakly similar properties.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498601&req=5

fig1: HMG-box sequence comparison. Sequence alignment of non-sequence-specific HMG-box proteins: HMGB1 (rat; rHMGB1-A, box A; rHMGB1-B, box B), HMGD (Drosophila), NHP6A (S. cerevisiae), sequence-specific/non-sequence-specific TFAM (human mitochondria; TFAM-HMG1, box A; TFAM-HMG2, box B) and sequence-specific SRY (human) and LEF1 (mouse). The three α-helices of the HMG box are shown above the alignment. Arrows indicate the 1° and 2° intercalating residues. Conserved residues (Clustal Omega alignment) are highlighted in gray, where an asterisk (*) indicates complete conservation, a colon (:) indicates conservation between groups with strongly similar properties and a dot (.) indicates conservation between groups with weakly similar properties.
Mentions: A hallmark of HMGB proteins is their ability to recognize the minor groove of pre-bent, distorted or linear DNA, bending linear DNA between 70 and 180° towards the major groove (Dragan et al., 2003 ▸, 2004 ▸; Werner et al., 1995 ▸). The HMGB1 domains are unequal in these properties: box A recognizes both pre-bent (Teo, Grasser & Thomas, 1995 ▸) and linear DNA more tightly than box B (Müller et al., 2001 ▸), but box B binds to mini-circles (Webb et al., 2001 ▸) and bends linear DNA to a greater extent than box A (Paull et al., 1993 ▸; Teo, Grasser & Thomas, 1995 ▸). This dramatic distortion of DNA is dependent on both shape complementarity and DNA intercalation of two apolar residues (Churchill et al., 2010 ▸; Klass et al., 2003 ▸; Murphy & Churchill, 2000 ▸; Roemer et al., 2008 ▸). The primary intercalation residue is in helix I (1° in Fig. 1 ▸) and the second intercalation wedge (2° in Fig. 1 ▸) is at the start of helix II. HMGB1 box A is an exception because Ala16 at the 1° site cannot intercalate DNA but Phe37 at the 2° site can, and this is thought to be responsible for the superior ability of box A to recognize pre-bent DNA (reviewed by Štros, 2010 ▸). Indeed, the crystal structure of box A bound to cisplatin intrastrand GG cross-linked DNA showed Phe37 lodged into the cisplatin-induced kink, although the DNA itself was relatively undistorted compared with the free cisplatin-modified DNA (Ohndorf et al., 1999 ▸). However, how box A recognizes natural, unmodified DNA remains unknown.

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