Journal:Acta Cryst D:S2059798321009633
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| - | <StructureSection load='' size='450' side='right' scene=' | + | <StructureSection load='' size='450' side='right' scene='89/895271/Cv/3' caption=''> |
===Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family=== | ===Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family=== | ||
| - | <big> | + | <big>Marketa Soltysova, Irena Sieglova, Milan Fabry, Jirı Brynda, Jana Skerlova |
| + | and Pavlına Rezacova</big> <ref>doi: 10.1107/S2059798321009633</ref> | ||
<hr/> | <hr/> | ||
<b>Molecular Tour</b><br> | <b>Molecular Tour</b><br> | ||
| + | SorC (SorC/DeoR) protein family (Pfam family Sugar-bind: PF04198<ref name="Finn">PMID:18039703</ref>) is one of the large families of bacterial transcriptional regulators, predominantly repressors, that are known for their roles in the regulation of carbohydrate metabolism and quorum-sensing in more than 2,500 bacterial species. For example, among the most studied members are CggR<ref name="Chaix">PMID:20462860</ref>,<ref name="Rezacova">PMID:18554327</ref>,<ref name="Zorilla">PMID:17293407</ref> or LsrR<ref name="Xavier">PMID:15601708</ref>,<ref name="Ha">PMID:24047255</ref>. SorC protomers consist of a large C terminal effector binding domain (EBD) and a much smaller N terminal DNA binding domain (DBD). As an assembly, SorC proteins work as tetramers in a cooperative manner, to our best knowledge<ref name="Zorilla">PMID:17293407</ref>,<ref name="Zeng">PMID:10714997</ref>. | ||
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| + | So far (2021), several 3D structures of SorC EBDs have been determined. They belong to the so-called NagB-like family for their homology with glucosamine 6 phosphate deaminases from the NagB family, characterized by the central Rossman fold<ref name="Rezacova">PMID:18554327</ref>,<ref name="Skerlova">PMID:24863636</ref>,<ref name="Sanctis">PMID:19232357</ref>. On the other hand, information on the structure of DNA-binding domains of SorC-family proteins is rather limited. SorC DBDs belong to the most abundant helix turn helix (HTH) superfamily and, by their sequences and structures, they cluster into two subfamilies: SorC/DeoR and SorC/CggR. | ||
| + | SorC/DeoR DBD is smaller and consists of the HTH bundle followed by a "β linker"<ref name="Sanctis">PMID:19232357</ref>, and the bigger SorC/CggR belong to the winged HTH family<ref name="Doan">PMID:12622823</ref>. | ||
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| + | In this paper, we present the first structure of SorC DBDs bound to DNA duplexes. We show DBD structures of representatives of each subfamily, <scene name='89/895271/Cv/4'>DeoR</scene> and <scene name='89/895271/Cv/7'>CggR</scene>, and compare their binding mode, which is likely common to all SorC family members. | ||
| + | *<scene name='89/895271/Cv/4'>A cartoon representation of the bsDeoRDBD dimer bound to the DNA operator</scene>. First monomer is colored in red and the second one is in salmon. | ||
| + | *<scene name='89/895271/Cv/7'>A cartoon representation of the bsCggRDBD dimer bound to the DNA operator</scene>. ''bs''CggRDBD comprises five α-helices and two β-strands, with a topology of four α-helices α1 (1–13), α2 (15–32), α3 (37–43) and α4 (48–61) followed by <scene name='89/895271/Cv/8'>a β-hairpin (called a wing) formed by β1 (64–66) and β2 (71–73)</scene> and continuing with a final α-helix (75–89) that links the N-terminal DBD to the C-terminal EBD (α-helices are colored in red, β-strands are in yellow and second monomer is in salmon). | ||
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| + | *<scene name='89/895271/Cv/15'>Morph showing the conformational change of bsDeoR-DBD upon DNA binding</scene>. DNA-free ''bs''DeoRDBD is colored in pink and DNA-bound ''bs''DeoRDBD is in red. <jmol><jmolButton> | ||
| + | <script>if (_animating); anim pause;set echo bottom left; color echo white; font echo 20 sansserif;echo Animation Paused; else; anim resume; set echo off;endif;</script> | ||
| + | <text>Stop Animation</text> | ||
| + | </jmolButton></jmol> | ||
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| + | '''PDB references:''' DNA-binding domain of DeoR in complex with DNA operator, [[7bhy]]; DNA-binding domain of CggR in complex with DNA operator, [[7oyk]]. | ||
<b>References</b><br> | <b>References</b><br> | ||
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