Proteopedia - User contributions [en]

https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Balagopal+Nithin Proteopedia - User contributions [en] 2026-09-15T23:36:06Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=NolR&diff=4396098 NolR 2025-11-30T04:41:39Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR (BI3323-Aug2025)</b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 and alpha-4</scene>) positions the recognition helix (<scene name='85/857155/Alpha3_alpha4/1'>alpha-3 and alpha-4</scene>) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (<scene name='85/857155/Dna/1'>Oligo AT</scene>) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=NolR&diff=4395846 NolR 2025-11-28T12:08:48Z

<p>Balagopal Nithin: New page: <table width="95%" border="0"><tr><td> {| align="left" |- | |} </td></tr><tr><td> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gen...</p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 and alpha-4</scene>) positions the recognition helix (<scene name='85/857155/Alpha3_alpha4/1'>alpha-3 and alpha-4</scene>) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (<scene name='85/857155/Dna/1'>Oligo AT</scene>) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395845 Sandbox 2025-11-28T12:02:17Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 and alpha-4</scene>) positions the recognition helix (<scene name='85/857155/Alpha3_alpha4/1'>alpha-3 and alpha-4</scene>) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (<scene name='85/857155/Dna/1'>Oligo AT</scene>) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395844 Sandbox 2025-11-28T11:59:45Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 and alpha-4</scene>) positions the recognition helix (<scene name='85/857155/Alpha3_alpha4/1'>alpha-3 and alpha-4</scene>) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395843 Sandbox 2025-11-28T11:55:18Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 and alpha-4</scene>) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395842 Sandbox 2025-11-28T11:54:35Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 to alpha-4</scene>) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395841 Sandbox 2025-11-28T11:49:21Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395840 Sandbox 2025-11-28T11:34:14Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.<br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395838 Sandbox 2025-11-28T11:14:10Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.<br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395837 Sandbox 2025-11-28T11:05:11Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> <br /> Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene><br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395829 Sandbox 2025-11-28T10:23:02Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene><br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395827 Sandbox 2025-11-28T10:17:48Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> Click on Chain A to visualize "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".<br /> Click on Chain B to visualize "Chain B" of "NolR".<br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene><br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395826 Sandbox 2025-11-28T10:10:04Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> <scene name='85/857155/Chain_a/1'>Chain_A</scene><br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene><br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395825 Sandbox 2025-11-28T09:05:44Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> <scene name="Chain_A">Show Overall Structure (PDB 4OMZ)</scene><br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene><br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395824 Sandbox 2025-11-28T07:32:36Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> <br /> <scene name="Overall_Structure">Show Overall Structure (PDB 4OMZ)</scene><br /> <br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> <br /> <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene><br /> <br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> <br /> <scene name="Gln56_Switch">Focus on Gln56 Switch</scene><br /> <br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395823 Sandbox 2025-11-28T07:22:07Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br><br /> University/Institution Name (Indian Institute of Science Education and Research,Pune)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4395822 Sandbox 2025-11-28T07:15:54Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen<br /> <br /> PNAS, March 6, 2025, Vol. 122 No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] <br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ===Abstract===<br /> The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.<br /> <br /> ===Overall Structure of NolR===<br /> NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.<br /> * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.<br /> * '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.<br /> * '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.<br /> <br /> ===DNA Binding and Recognition===<br /> The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.<br /> * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.<br /> * '''Minor Groove:''' The beta-wing residues contact the minor groove.<br /> * '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.<br /> * '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.<br /> <br /> ===The Gln56 Conformational Switch===<br /> A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).<br /> * '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.<br /> * '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.<br /> <br /> ===References===<br /> * Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.<br /> <br /> ===About this Page===<br /> <br /> This page was created by '''[[User:Your_Username|Your Name Here]]'''.<br><br /> University/Institution Name (Optional)<br /> <br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4392076 Sandbox 2025-11-13T14:01:31Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> <br /> PNAS, April 29, 2014, Vol. 111, No.17[https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ==Structural and Biological Significance==<br /> ===Global Regulation of Nitrogen Fixation Symbiosis===<br /> NolR is a transcriptional regulator that fine-tunes the expression of nodulation (nod) and symbiosis genes across diverse Rhizobium species. Despite its critical ecological importance, the molecular basis of NolR's regulatory mechanism remained largely unknown until the comprehensive structural characterization presented in this paper.<br /> === Structural Architecture and DNA-Binding Mechanism===<br /> The crystallographic structures of NolR reveal a homodimeric winged '''helix-turn-helix''' transcription factor, comprising two α-helical regions ('''α1 and α5''') forming the dimerization interface and a triangular configuration of helices ('''α2–α4''') that positions the conserved helix-turn-helix motif ('''α3–α4''') for DNA major groove binding. Notably, a distinctive "wing" composed of antiparallel β-sheets extends into the DNA minor groove. This architectural arrangement enables NolR to recognize '''asymmetric operator sequences'''—a remarkable feature that confers specificity and versatility in binding diverse target genes.<br /> ===The Gln56 Conformational Switch: A Novel Regulatory Innovation===<br /> Perhaps the most striking discovery of this work is the identification of a **conformational switching mechanism** centered on **glutamine residue 56 (Gln56)**. This glutamine adopts different conformational states depending on the nucleotide composition of target DNA sequences. In the first half-site of the operator, Gln56 orients toward the adenine base (A2), while in the second half-site, its side-chain can flip away from thymine (T7') or reorient toward adenine (A7') depending on the sequence variation.<br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390300 Sandbox 2025-11-11T18:26:45Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> <br /> PNAS, April 29, 2014, Vol. 111, No.17[https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ==Structural and Biological Significance==<br /> ===Global Regulation of Nitrogen Fixation Symbiosis===<br /> NolR is a transcriptional regulator that fine-tunes the expression of nodulation (nod) and symbiosis genes across diverse Rhizobium species. Despite its critical ecological importance, the molecular basis of NolR's regulatory mechanism remained largely unknown until the comprehensive structural characterization presented in this paper.<br /> === Structural Architecture and DNA-Binding Mechanism===<br /> The crystallographic structures of NolR reveal a homodimeric winged '''helix-turn-helix''' transcription factor, comprising two α-helical regions ('''α1 and α5''') forming the dimerization interface and a triangular configuration of helices ('''α2–α4''') that positions the conserved helix-turn-helix motif ('''α3–α4''') for DNA major groove binding. Notably, a distinctive "wing" composed of antiparallel β-sheets extends into the DNA minor groove. This architectural arrangement enables NolR to recognize '''asymmetric operator sequences'''—a remarkable feature that confers specificity and versatility in binding diverse target genes.<br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390299 Sandbox 2025-11-11T17:58:34Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> <br /> PNAS, April 29, 2014, Vol. 111, No.17[https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ==Background==<br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390294 Sandbox 2025-11-10T20:27:31Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> [https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> <br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> ==Background==<br /> <br /> </StructureSection></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390293 Sandbox 2025-11-10T20:22:07Z

<p>Balagopal Nithin: </p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> [https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==<br /> ==NolR==<br /> <StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''><br /> <br /> Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br /> <br /> </StructureSection><br /> ===Background===</div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390292 Sandbox 2025-11-10T20:11:36Z

<p>Balagopal Nithin: Replacing page with '<table width="95%" border="0"><tr><td> {| align="left" |- | |} </td></tr><tr><td> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and s...'</p> <hr /> <div><table width="95%" border="0"><tr><td><br /> {| align="left"<br /> |-<br /> |<br /> |}<br /> </td></tr><tr><td><br /> <br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span><br /> </td></tr><tr><td><br /> <br /> <span style="font-size:120%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> [https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> <br /> ==Structure Tour==</div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390291 Sandbox 2025-11-10T19:48:48Z

<p>Balagopal Nithin: </p> <hr /> <div><span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation<br /> and symbiosis gene expression by the regulatory<br /> protein NolR.</b></span><br /> <br /> <br /> <span style="font-size:100%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> <br /> [https://doi.org/10.1073/pnas.1402243111] (2014).<br /> [https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> <br /> </td></tr></table><br /> __NOTOC__<br /> ==Structure Tour==<br /> <StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/7'><br /> ===Background===<br /> Previously, pili of ''Geobacter sulfurreducens'' were thought to be composed of PilA-N, a 61-amino acid protein<ref name="blindmen">PMID: 33070100</ref><ref name="homolmod">PMID: 25736881 </ref><ref name="lovleyreview">PMID: 31608018 </ref>. Immediately downstream from the ''pilA-N'' gene is ''pilA-C'', coding for a 104 amino acid protein suspected to be the missing C-terminal globular domain of PilA-N<ref>PMID:22408162 </ref><ref>PMID:28348867</ref>. Gene fission of pilins is widely distributed in ''Desulfuromonadales'' including ''Geobacteracae''<ref>PMID: 28066394</ref>. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported<ref name="nw1">PMID: 30951668</ref><ref name="nw2">PMID: 31925024</ref><ref name="omcz">PMID: 32807967</ref>.<br /> <br /> ===Pilus Structure===<br /> <br /> {{Template:ClickGreenLinks}}<br /> <br /> Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili (<scene name='83/834714/Filament/7'>restore initial scene</scene>), [[6vk9]], reveals them to be <scene name='83/834714/Filament/9'>composed of a core</scene> of '''<font color='#e87000'>PilA-N</font>''' (61 amino acids) coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids). Here is a <scene name='83/834714/Filament/10'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.<br /> <br /> The '''PilA-N''' subunits have extensive hydrophobic contacts with each other, stabilizing the hydrophobic core of the filament. <scene name='83/834714/Filament/11'>View PilA-N with PilA-C hidden</scene>. Each PilA-N chain contacts 75 carbon atoms from 11 adjacent PilA-N chains, and also has 4 hydrogen bonds and 4 salt bridges with adjacent PilA-N chains (not shown). In contrast, '''PilA-C''' subunits (<scene name='83/834714/Filament/12'>view PilA-C with front half and PilA-N hidden</scene>) have little contact with each other: 14 atoms, which are mostly hydrogen bonded, with one salt bridge (not shown).<br /> <br /> ===Heterodimers===<br /> <br /> The pilus filament is assembled from <scene name='83/834714/Dimer/5'>heterodimers</scene>. Dimer <scene name='83/834714/Dimer/6'>secondary structure</scene>: '''<font color='#e87000'>PilA-N</font>''' consists of two alpha helices, while '''<font color='00a0a0'>PilA-C</font>''' includes a 3-stranded beta sheet. The C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>''' is <scene name='83/834714/Flaps/7'>held between two flaps</scene> (darker) of '''<font color='00a0a0'>PilA-C</font>'''. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>'''. These flaps might be open before '''<font color='#e87000'>PilA-N</font>''' arrives to form a dimer, reminiscent of the flaps of HIV protease<ref>PMID: 16418268</ref>. (See, for example, [[1hxw]] and [[Flaps Morph for HIV Protease]].) <scene name='83/834714/Flaps/8'>Four glycines</scene> (<font color="red">'''red: 10, 11, 31, 37'''</font>) provide flexibility that could enable opening of the flaps. <br /> <br /> ===Other Findings and Conclusions===<br /> <br /> As detailed in the journal publication, the PilA-N-C pili studied here are 20-fold less electrically conductive than the nanowires composed of OmcS cytochromes<ref name="nw1" /><ref name="nw2" />, and 20,000-fold less conductive than OmcZ nanowires<ref name="omcz" />. These PilA-N-C pili lack the structural hallmarks of type 4 pili, but share structural characteristics with pseudopili. PilA-N and PilA-C remain in the inner membrane, unless the gene for OmcS (or OmcZ) is deleted, in which case they form the pili extending outside the cell studied here. When the ''pilA-N'' gene is deleted, OmcS nanowires fail to be produced. It is proposed in the journal publication that PilA-N-C is part of a secretion system required for production of OmcS/OmcZ nanowires.<br /> <br /> <br /> </StructureSection><br /> <br /> <br><br /> <hr><br><br /> <br /> ==See Also==<br /> * [[6vk9]], the structure described here.<br /> * [[Malvankar]]: A list of all interactive 3D complements for publications from the Malvankar group, including:<br /> ** Structure of the OmcS conductive nanowire: [[Malvankar/2|2019, Cell: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.]]<br /> <br /> ==Notes & References==<br /> <references /></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390290 Sandbox 2025-11-10T19:47:52Z

<p>Balagopal Nithin: </p> <hr /> <div><span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation<br /> and symbiosis gene expression by the regulatory<br /> protein NolR.</b></span><br /> <br /> <br /> <span style="font-size:100%"><br /> Soon Goo Lee, Hari B.Krishnan and Joseph M.Jez<br /> <br /> [https://doi.org/10.1073/pnas.1402243111] (2014).<br /> [https://doi.org/10.1073/pnas.1402243111]<br /> </span><br /> </td></tr></table><br /> __NOTOC__<br /> ==Structure Tour==<br /> <StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/7'><br /> ===Background===<br /> Previously, pili of ''Geobacter sulfurreducens'' were thought to be composed of PilA-N, a 61-amino acid protein<ref name="blindmen">PMID: 33070100</ref><ref name="homolmod">PMID: 25736881 </ref><ref name="lovleyreview">PMID: 31608018 </ref>. Immediately downstream from the ''pilA-N'' gene is ''pilA-C'', coding for a 104 amino acid protein suspected to be the missing C-terminal globular domain of PilA-N<ref>PMID:22408162 </ref><ref>PMID:28348867</ref>. Gene fission of pilins is widely distributed in ''Desulfuromonadales'' including ''Geobacteracae''<ref>PMID: 28066394</ref>. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported<ref name="nw1">PMID: 30951668</ref><ref name="nw2">PMID: 31925024</ref><ref name="omcz">PMID: 32807967</ref>.<br /> <br /> ===Pilus Structure===<br /> <br /> {{Template:ClickGreenLinks}}<br /> <br /> Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili (<scene name='83/834714/Filament/7'>restore initial scene</scene>), [[6vk9]], reveals them to be <scene name='83/834714/Filament/9'>composed of a core</scene> of '''<font color='#e87000'>PilA-N</font>''' (61 amino acids) coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids). Here is a <scene name='83/834714/Filament/10'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.<br /> <br /> The '''PilA-N''' subunits have extensive hydrophobic contacts with each other, stabilizing the hydrophobic core of the filament. <scene name='83/834714/Filament/11'>View PilA-N with PilA-C hidden</scene>. Each PilA-N chain contacts 75 carbon atoms from 11 adjacent PilA-N chains, and also has 4 hydrogen bonds and 4 salt bridges with adjacent PilA-N chains (not shown). In contrast, '''PilA-C''' subunits (<scene name='83/834714/Filament/12'>view PilA-C with front half and PilA-N hidden</scene>) have little contact with each other: 14 atoms, which are mostly hydrogen bonded, with one salt bridge (not shown).<br /> <br /> ===Heterodimers===<br /> <br /> The pilus filament is assembled from <scene name='83/834714/Dimer/5'>heterodimers</scene>. Dimer <scene name='83/834714/Dimer/6'>secondary structure</scene>: '''<font color='#e87000'>PilA-N</font>''' consists of two alpha helices, while '''<font color='00a0a0'>PilA-C</font>''' includes a 3-stranded beta sheet. The C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>''' is <scene name='83/834714/Flaps/7'>held between two flaps</scene> (darker) of '''<font color='00a0a0'>PilA-C</font>'''. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>'''. These flaps might be open before '''<font color='#e87000'>PilA-N</font>''' arrives to form a dimer, reminiscent of the flaps of HIV protease<ref>PMID: 16418268</ref>. (See, for example, [[1hxw]] and [[Flaps Morph for HIV Protease]].) <scene name='83/834714/Flaps/8'>Four glycines</scene> (<font color="red">'''red: 10, 11, 31, 37'''</font>) provide flexibility that could enable opening of the flaps. <br /> <br /> ===Other Findings and Conclusions===<br /> <br /> As detailed in the journal publication, the PilA-N-C pili studied here are 20-fold less electrically conductive than the nanowires composed of OmcS cytochromes<ref name="nw1" /><ref name="nw2" />, and 20,000-fold less conductive than OmcZ nanowires<ref name="omcz" />. These PilA-N-C pili lack the structural hallmarks of type 4 pili, but share structural characteristics with pseudopili. PilA-N and PilA-C remain in the inner membrane, unless the gene for OmcS (or OmcZ) is deleted, in which case they form the pili extending outside the cell studied here. When the ''pilA-N'' gene is deleted, OmcS nanowires fail to be produced. It is proposed in the journal publication that PilA-N-C is part of a secretion system required for production of OmcS/OmcZ nanowires.<br /> <br /> <br /> </StructureSection><br /> <br /> <br><br /> <hr><br><br /> <br /> ==See Also==<br /> * [[6vk9]], the structure described here.<br /> * [[Malvankar]]: A list of all interactive 3D complements for publications from the Malvankar group, including:<br /> ** Structure of the OmcS conductive nanowire: [[Malvankar/2|2019, Cell: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.]]<br /> <br /> ==Notes & References==<br /> <references /></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390289 Sandbox 2025-11-10T19:37:50Z

<p>Balagopal Nithin: </p> <hr /> <div><br /> <span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation<br /> and symbiosis gene expression by the regulatory<br /> protein NolR.</b></span><br /> <br /> <br /> <span style="font-size:100%"><br /> [[User:Yangqi Gu|Yangqi '''Gu''']],<br /> [[User:Vishok Srikanth|Vishok '''Srikanth''']],<br /> Aldo I. '''[https://www.linkedin.com/in/aldo-salazar-morales-7a866617 Salazar-Morales]''',<br /> Ruchi '''Jain''',<br /> J. Patrick '''[https://malvankarlab.yale.edu/group-members O'Brien]''',<br /> Sophia M. '''[https://malvankarlab.yale.edu/group-members Yi]''',<br /> Rajesh K. '''Soni''',<br /> Fadel A. [[User:Fadel A. Samatey|'''Samatey''']],<br /> Sibel Ebru '''[https://medicine.yale.edu/profile/sibel_yalcin/ Yalcin]''',<br /> and Nikhil S. '''[[User:Nikhil_Malvankar|Malvankar]]'''.<br /> [https://www.nature.com/articles/s41586-021-03857-w nature.com/articles/s41586-021-03857-w] (2021).<br /> [https://doi.org/10.1038/s41586-021-03857-w DOI 10.1038/s41586-021-03857-w]<br /> </span><br /> </td></tr></table><br /> __NOTOC__<br /> ==Structure Tour==<br /> <StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/7'><br /> ===Background===<br /> Previously, pili of ''Geobacter sulfurreducens'' were thought to be composed of PilA-N, a 61-amino acid protein<ref name="blindmen">PMID: 33070100</ref><ref name="homolmod">PMID: 25736881 </ref><ref name="lovleyreview">PMID: 31608018 </ref>. Immediately downstream from the ''pilA-N'' gene is ''pilA-C'', coding for a 104 amino acid protein suspected to be the missing C-terminal globular domain of PilA-N<ref>PMID:22408162 </ref><ref>PMID:28348867</ref>. Gene fission of pilins is widely distributed in ''Desulfuromonadales'' including ''Geobacteracae''<ref>PMID: 28066394</ref>. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported<ref name="nw1">PMID: 30951668</ref><ref name="nw2">PMID: 31925024</ref><ref name="omcz">PMID: 32807967</ref>.<br /> <br /> ===Pilus Structure===<br /> <br /> {{Template:ClickGreenLinks}}<br /> <br /> Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili (<scene name='83/834714/Filament/7'>restore initial scene</scene>), [[6vk9]], reveals them to be <scene name='83/834714/Filament/9'>composed of a core</scene> of '''<font color='#e87000'>PilA-N</font>''' (61 amino acids) coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids). Here is a <scene name='83/834714/Filament/10'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.<br /> <br /> The '''PilA-N''' subunits have extensive hydrophobic contacts with each other, stabilizing the hydrophobic core of the filament. <scene name='83/834714/Filament/11'>View PilA-N with PilA-C hidden</scene>. Each PilA-N chain contacts 75 carbon atoms from 11 adjacent PilA-N chains, and also has 4 hydrogen bonds and 4 salt bridges with adjacent PilA-N chains (not shown). In contrast, '''PilA-C''' subunits (<scene name='83/834714/Filament/12'>view PilA-C with front half and PilA-N hidden</scene>) have little contact with each other: 14 atoms, which are mostly hydrogen bonded, with one salt bridge (not shown).<br /> <br /> ===Heterodimers===<br /> <br /> The pilus filament is assembled from <scene name='83/834714/Dimer/5'>heterodimers</scene>. Dimer <scene name='83/834714/Dimer/6'>secondary structure</scene>: '''<font color='#e87000'>PilA-N</font>''' consists of two alpha helices, while '''<font color='00a0a0'>PilA-C</font>''' includes a 3-stranded beta sheet. The C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>''' is <scene name='83/834714/Flaps/7'>held between two flaps</scene> (darker) of '''<font color='00a0a0'>PilA-C</font>'''. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>'''. These flaps might be open before '''<font color='#e87000'>PilA-N</font>''' arrives to form a dimer, reminiscent of the flaps of HIV protease<ref>PMID: 16418268</ref>. (See, for example, [[1hxw]] and [[Flaps Morph for HIV Protease]].) <scene name='83/834714/Flaps/8'>Four glycines</scene> (<font color="red">'''red: 10, 11, 31, 37'''</font>) provide flexibility that could enable opening of the flaps. <br /> <br /> ===Other Findings and Conclusions===<br /> <br /> As detailed in the journal publication, the PilA-N-C pili studied here are 20-fold less electrically conductive than the nanowires composed of OmcS cytochromes<ref name="nw1" /><ref name="nw2" />, and 20,000-fold less conductive than OmcZ nanowires<ref name="omcz" />. These PilA-N-C pili lack the structural hallmarks of type 4 pili, but share structural characteristics with pseudopili. PilA-N and PilA-C remain in the inner membrane, unless the gene for OmcS (or OmcZ) is deleted, in which case they form the pili extending outside the cell studied here. When the ''pilA-N'' gene is deleted, OmcS nanowires fail to be produced. It is proposed in the journal publication that PilA-N-C is part of a secretion system required for production of OmcS/OmcZ nanowires.<br /> <br /> <br /> </StructureSection><br /> <br /> <br><br /> <hr><br><br /> <br /> ==See Also==<br /> * [[6vk9]], the structure described here.<br /> * [[Malvankar]]: A list of all interactive 3D complements for publications from the Malvankar group, including:<br /> ** Structure of the OmcS conductive nanowire: [[Malvankar/2|2019, Cell: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.]]<br /> <br /> ==Notes & References==<br /> <references /></div>

Balagopal Nithin https://proteopedia.org/index.php?title=Sandbox&diff=4390288 Sandbox 2025-11-10T19:17:17Z

<p>Balagopal Nithin: </p> <hr /> <div>== NolR ==<br /> <br /> The symbiosis between rhizobial microbes and legume plants is fundamental to sustainable agriculture and ecological nitrogen cycling. This partnership requires coordinated expression of multiple genes to establish nitrogen-fixing nodules, with **NolR serving as a global transcriptional regulator** controlling this critical developmental process across diverse *Rhizobium* species.<br /> <br /> We present the first high-resolution X-ray crystal structures of NolR in both unliganded and DNA-bound forms, revealing its complex interactions with asymmetric operator sequences. Analysis of NolR complexed with two different 22-base pair operator DNA sequences (oligos AT and AA) demonstrates that this **homodimeric transcription factor adopts a winged helix-turn-helix fold** and recognizes DNA through a combination of positively charged surface residues that engage the DNA phosphate backbone and specific base contacts.<br /> <br /> The most striking finding is a **conformational switching mechanism involving Gln56**, which alters its position to accommodate variation in target DNA sequences without changing overall binding affinity. This elegant mechanism allows NolR to regulate multiple nodulation and symbiosis genes with different operator sequences through modulation of thermodynamic binding contributions. The conformational flexibility of this key residue represents a novel regulatory strategy in the ArsR/SmtB transcription factor family.<br /> <br /> These structural studies provide unprecedented molecular insight into **how NolR functions as a global regulatory hub**, proposing two distinct regulatory models for differential gene expression during nodule formation and symbiotic nitrogen fixation. This work illuminates the structural basis for one of nature's most important agricultural and ecological partnerships.</div>

Balagopal Nithin