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Crystal structure of a two-subunit TrkA octameric gating ring assembly.

Deller MC, Johnson HA, Miller MD, Spraggon G, Elsliger MA, Wilson IA, Lesley SA - PLoS ONE (2015)

Bottom Line: TM1088 represents the first structure of a two-subunit Trk assembly.Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies.This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies.

View Article: PubMed Central - PubMed

Affiliation: The Joint Center for Structural Genomics, and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America.

ABSTRACT
The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K+ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K+ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K+ ions across the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies.

No MeSH data available.


Crystal structures of TM1088 proteins.(A) Ribbon representation of the high-resolution structure of TM1088A showing some of the conserved hydrophobic residues involved in dimer formation (Ile130, Val133 and Ile138 as red sticks. Bound AMP is displayed as yellow spheres. Sequence logo of the nucleotide binding motif region (Gly14/Gly16/Gly19) from structural alignment with other nucleotide binding RCK family members is shown inset (PDB ID: 1LSS and 1LSU). Each position of the sequence is represented by a stack of residues with the height of each stack representing the conservation at that position. Glycine and polar amino acids are colored green, basic amino acids are colored blue and hydrophobic amino acids are colored black [47]. (B) Ribbon representation of the TM1088A dimer of the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Phe88, Met91, Ile114 and Phe115). The “dimer hinge” angle is denoted by a red arrow. (C) Ribbon representation of the TM1088B dimer from the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Leu80, Phe81 and Met111). Sequence logo of the structurally equivalent region to the AMP binding site of TM1088A is shown inset. A structural alignment of non-nucleotide binding RCK family members (PDB ID: 1ID1 and 1LNQ) was used for the alignment. (D) Ribbon representation of the TM1088B C-terminal domain. Conserved hydrophobic residues involved in the TM1088B dimer interface are shown as red sticks (Ile140, Phe148, Ile174, Val179, Tyr200 and Ile202).
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pone.0122512.g002: Crystal structures of TM1088 proteins.(A) Ribbon representation of the high-resolution structure of TM1088A showing some of the conserved hydrophobic residues involved in dimer formation (Ile130, Val133 and Ile138 as red sticks. Bound AMP is displayed as yellow spheres. Sequence logo of the nucleotide binding motif region (Gly14/Gly16/Gly19) from structural alignment with other nucleotide binding RCK family members is shown inset (PDB ID: 1LSS and 1LSU). Each position of the sequence is represented by a stack of residues with the height of each stack representing the conservation at that position. Glycine and polar amino acids are colored green, basic amino acids are colored blue and hydrophobic amino acids are colored black [47]. (B) Ribbon representation of the TM1088A dimer of the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Phe88, Met91, Ile114 and Phe115). The “dimer hinge” angle is denoted by a red arrow. (C) Ribbon representation of the TM1088B dimer from the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Leu80, Phe81 and Met111). Sequence logo of the structurally equivalent region to the AMP binding site of TM1088A is shown inset. A structural alignment of non-nucleotide binding RCK family members (PDB ID: 1ID1 and 1LNQ) was used for the alignment. (D) Ribbon representation of the TM1088B C-terminal domain. Conserved hydrophobic residues involved in the TM1088B dimer interface are shown as red sticks (Ile140, Phe148, Ile174, Val179, Tyr200 and Ile202).

Mentions: The crystal structures of full-length TM1088A (Fig 2A–2B and Table 1, PDB ID: 2G1U) and the C-terminal domain of TM1088B (Fig 2C–2D and Table 1, PDB ID: 3JXO) were determined to 1.50 Å and 1.55 Å, respectively. The overall fold, dimer-interfaces and arrangement of these higher resolution structures are consistent with the corresponding components in the octameric TM1088 assembly.


Crystal structure of a two-subunit TrkA octameric gating ring assembly.

Deller MC, Johnson HA, Miller MD, Spraggon G, Elsliger MA, Wilson IA, Lesley SA - PLoS ONE (2015)

Crystal structures of TM1088 proteins.(A) Ribbon representation of the high-resolution structure of TM1088A showing some of the conserved hydrophobic residues involved in dimer formation (Ile130, Val133 and Ile138 as red sticks. Bound AMP is displayed as yellow spheres. Sequence logo of the nucleotide binding motif region (Gly14/Gly16/Gly19) from structural alignment with other nucleotide binding RCK family members is shown inset (PDB ID: 1LSS and 1LSU). Each position of the sequence is represented by a stack of residues with the height of each stack representing the conservation at that position. Glycine and polar amino acids are colored green, basic amino acids are colored blue and hydrophobic amino acids are colored black [47]. (B) Ribbon representation of the TM1088A dimer of the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Phe88, Met91, Ile114 and Phe115). The “dimer hinge” angle is denoted by a red arrow. (C) Ribbon representation of the TM1088B dimer from the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Leu80, Phe81 and Met111). Sequence logo of the structurally equivalent region to the AMP binding site of TM1088A is shown inset. A structural alignment of non-nucleotide binding RCK family members (PDB ID: 1ID1 and 1LNQ) was used for the alignment. (D) Ribbon representation of the TM1088B C-terminal domain. Conserved hydrophobic residues involved in the TM1088B dimer interface are shown as red sticks (Ile140, Phe148, Ile174, Val179, Tyr200 and Ile202).
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pone.0122512.g002: Crystal structures of TM1088 proteins.(A) Ribbon representation of the high-resolution structure of TM1088A showing some of the conserved hydrophobic residues involved in dimer formation (Ile130, Val133 and Ile138 as red sticks. Bound AMP is displayed as yellow spheres. Sequence logo of the nucleotide binding motif region (Gly14/Gly16/Gly19) from structural alignment with other nucleotide binding RCK family members is shown inset (PDB ID: 1LSS and 1LSU). Each position of the sequence is represented by a stack of residues with the height of each stack representing the conservation at that position. Glycine and polar amino acids are colored green, basic amino acids are colored blue and hydrophobic amino acids are colored black [47]. (B) Ribbon representation of the TM1088A dimer of the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Phe88, Met91, Ile114 and Phe115). The “dimer hinge” angle is denoted by a red arrow. (C) Ribbon representation of the TM1088B dimer from the octameric TM1088 assembly. Conserved hydrophobic residues involved in the TM1088A to TM1088B interface are shown as red sticks (Leu80, Phe81 and Met111). Sequence logo of the structurally equivalent region to the AMP binding site of TM1088A is shown inset. A structural alignment of non-nucleotide binding RCK family members (PDB ID: 1ID1 and 1LNQ) was used for the alignment. (D) Ribbon representation of the TM1088B C-terminal domain. Conserved hydrophobic residues involved in the TM1088B dimer interface are shown as red sticks (Ile140, Phe148, Ile174, Val179, Tyr200 and Ile202).
Mentions: The crystal structures of full-length TM1088A (Fig 2A–2B and Table 1, PDB ID: 2G1U) and the C-terminal domain of TM1088B (Fig 2C–2D and Table 1, PDB ID: 3JXO) were determined to 1.50 Å and 1.55 Å, respectively. The overall fold, dimer-interfaces and arrangement of these higher resolution structures are consistent with the corresponding components in the octameric TM1088 assembly.

Bottom Line: TM1088 represents the first structure of a two-subunit Trk assembly.Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies.This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies.

View Article: PubMed Central - PubMed

Affiliation: The Joint Center for Structural Genomics, and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America.

ABSTRACT
The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K+ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K+ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K+ ions across the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies.

No MeSH data available.