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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.


Related in: MedlinePlus

Potential role of TM1088 interfaces in the gating ring assembly.(A) The two unique dimers of the TM1088 assembly are highlighted (red dashed lobes) showing the three unique protein:protein interfaces (orange and red curves). The “dimer hinge 1” between TM1008B dimer partners (red arrow), “dimer hinge 2” between TM1088A dimer partners (red arrow) and the “mobile or fixed” interface between adjacent dimer pairs (orange curve) are shown. (B) “Dimer hinge 2” between the N-terminal Trk domains N2 and N2’ of TM1088A. (C) “Dimer hinge 1” between N-terminal Trk domains N1 and C1, and N1’ and C1’ of TM1088B. (D) “Mobile or fixed” interface between adjacent TM1088A and TM1088B dimer pairs. TM1088A helices are shown in green (α3: Asp83-Phe97 and α4: Ile112-Asn118) and TM1088B helices in blue (α4: Ile82-Asp76 and α6: Ile107-Met111). Conserved hydrophobic residues are shown as green sticks (TM1088A: Phe88, Met91 and Ile114) and blue sticks (TM1088B: Leu80, Phe81, Met111). The “helix crossover” angle between α3 of TM1088A and α4 of TM1088B is denoted by an orange arrow. (E) The single unique dimer of the TrkA assembly (PDB ID: 4J9U) is highlighted showing the three unique protein interfaces (orange and red curves). The “dimer hinge” angle between dimer partners for the closed conformation (red dashed line, ADP-bound TrkA, PDB ID: 4J9U) and the open conformation (green dashed line, ATPγS-bound TrkA, PDB ID: 4J9V) are shown.
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pone.0122512.g006: Potential role of TM1088 interfaces in the gating ring assembly.(A) The two unique dimers of the TM1088 assembly are highlighted (red dashed lobes) showing the three unique protein:protein interfaces (orange and red curves). The “dimer hinge 1” between TM1008B dimer partners (red arrow), “dimer hinge 2” between TM1088A dimer partners (red arrow) and the “mobile or fixed” interface between adjacent dimer pairs (orange curve) are shown. (B) “Dimer hinge 2” between the N-terminal Trk domains N2 and N2’ of TM1088A. (C) “Dimer hinge 1” between N-terminal Trk domains N1 and C1, and N1’ and C1’ of TM1088B. (D) “Mobile or fixed” interface between adjacent TM1088A and TM1088B dimer pairs. TM1088A helices are shown in green (α3: Asp83-Phe97 and α4: Ile112-Asn118) and TM1088B helices in blue (α4: Ile82-Asp76 and α6: Ile107-Met111). Conserved hydrophobic residues are shown as green sticks (TM1088A: Phe88, Met91 and Ile114) and blue sticks (TM1088B: Leu80, Phe81, Met111). The “helix crossover” angle between α3 of TM1088A and α4 of TM1088B is denoted by an orange arrow. (E) The single unique dimer of the TrkA assembly (PDB ID: 4J9U) is highlighted showing the three unique protein interfaces (orange and red curves). The “dimer hinge” angle between dimer partners for the closed conformation (red dashed line, ADP-bound TrkA, PDB ID: 4J9U) and the open conformation (green dashed line, ATPγS-bound TrkA, PDB ID: 4J9V) are shown.

Mentions: Surprisingly, the atypical two-subunit structure of the TM1088 assembly results in three unique protein:protein interfaces that are all structurally homologous to interfaces known to be central to gating ring assembly in the RCK family of K+ transport proteins (Fig 6A). These interfaces are classically characterized as being either a) an intra-chain flexible “dimer hinge” between RCK domains or b) a “mobile” or “fixed” inter-chain interface between neighboring RCK domains. Interestingly, as a result of its two-subunit nature, the TM1088 assembly has an additional “dimer hinge” not observed in other gating ring assemblies (Fig 6A). The N1:N1’ interface of the TM1088B dimer forms “dimer hinge 1” that is analogous to the more classical dimer hinge between the N- and C-terminal domains as observed in TrkA, BK and MthK assemblies. The N2:N2’ interface of the TM1088A dimer forms “dimer hinge 2” (Fig 6A). The third interface between adjacent TM1088A and TM1088B dimer pairs (N1:N2’) is structurally analogous to the “mobile” or “fixed” interfaces of other K+ gating ring assemblies (Fig 6A). The “dimer hinge” angles of TM1088A and TM1088B are ~120° (Fig 6B and 6C, respectively). The “mobile or fixed” interface of TM1088, which can be measured as the “helix-crossover” angle between TM1088B and TM1088A dimers is measured as ~80° (Fig 6D).


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)

Potential role of TM1088 interfaces in the gating ring assembly.(A) The two unique dimers of the TM1088 assembly are highlighted (red dashed lobes) showing the three unique protein:protein interfaces (orange and red curves). The “dimer hinge 1” between TM1008B dimer partners (red arrow), “dimer hinge 2” between TM1088A dimer partners (red arrow) and the “mobile or fixed” interface between adjacent dimer pairs (orange curve) are shown. (B) “Dimer hinge 2” between the N-terminal Trk domains N2 and N2’ of TM1088A. (C) “Dimer hinge 1” between N-terminal Trk domains N1 and C1, and N1’ and C1’ of TM1088B. (D) “Mobile or fixed” interface between adjacent TM1088A and TM1088B dimer pairs. TM1088A helices are shown in green (α3: Asp83-Phe97 and α4: Ile112-Asn118) and TM1088B helices in blue (α4: Ile82-Asp76 and α6: Ile107-Met111). Conserved hydrophobic residues are shown as green sticks (TM1088A: Phe88, Met91 and Ile114) and blue sticks (TM1088B: Leu80, Phe81, Met111). The “helix crossover” angle between α3 of TM1088A and α4 of TM1088B is denoted by an orange arrow. (E) The single unique dimer of the TrkA assembly (PDB ID: 4J9U) is highlighted showing the three unique protein interfaces (orange and red curves). The “dimer hinge” angle between dimer partners for the closed conformation (red dashed line, ADP-bound TrkA, PDB ID: 4J9U) and the open conformation (green dashed line, ATPγS-bound TrkA, PDB ID: 4J9V) are shown.
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Related In: Results  -  Collection

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pone.0122512.g006: Potential role of TM1088 interfaces in the gating ring assembly.(A) The two unique dimers of the TM1088 assembly are highlighted (red dashed lobes) showing the three unique protein:protein interfaces (orange and red curves). The “dimer hinge 1” between TM1008B dimer partners (red arrow), “dimer hinge 2” between TM1088A dimer partners (red arrow) and the “mobile or fixed” interface between adjacent dimer pairs (orange curve) are shown. (B) “Dimer hinge 2” between the N-terminal Trk domains N2 and N2’ of TM1088A. (C) “Dimer hinge 1” between N-terminal Trk domains N1 and C1, and N1’ and C1’ of TM1088B. (D) “Mobile or fixed” interface between adjacent TM1088A and TM1088B dimer pairs. TM1088A helices are shown in green (α3: Asp83-Phe97 and α4: Ile112-Asn118) and TM1088B helices in blue (α4: Ile82-Asp76 and α6: Ile107-Met111). Conserved hydrophobic residues are shown as green sticks (TM1088A: Phe88, Met91 and Ile114) and blue sticks (TM1088B: Leu80, Phe81, Met111). The “helix crossover” angle between α3 of TM1088A and α4 of TM1088B is denoted by an orange arrow. (E) The single unique dimer of the TrkA assembly (PDB ID: 4J9U) is highlighted showing the three unique protein interfaces (orange and red curves). The “dimer hinge” angle between dimer partners for the closed conformation (red dashed line, ADP-bound TrkA, PDB ID: 4J9U) and the open conformation (green dashed line, ATPγS-bound TrkA, PDB ID: 4J9V) are shown.
Mentions: Surprisingly, the atypical two-subunit structure of the TM1088 assembly results in three unique protein:protein interfaces that are all structurally homologous to interfaces known to be central to gating ring assembly in the RCK family of K+ transport proteins (Fig 6A). These interfaces are classically characterized as being either a) an intra-chain flexible “dimer hinge” between RCK domains or b) a “mobile” or “fixed” inter-chain interface between neighboring RCK domains. Interestingly, as a result of its two-subunit nature, the TM1088 assembly has an additional “dimer hinge” not observed in other gating ring assemblies (Fig 6A). The N1:N1’ interface of the TM1088B dimer forms “dimer hinge 1” that is analogous to the more classical dimer hinge between the N- and C-terminal domains as observed in TrkA, BK and MthK assemblies. The N2:N2’ interface of the TM1088A dimer forms “dimer hinge 2” (Fig 6A). The third interface between adjacent TM1088A and TM1088B dimer pairs (N1:N2’) is structurally analogous to the “mobile” or “fixed” interfaces of other K+ gating ring assemblies (Fig 6A). The “dimer hinge” angles of TM1088A and TM1088B are ~120° (Fig 6B and 6C, respectively). The “mobile or fixed” interface of TM1088, which can be measured as the “helix-crossover” angle between TM1088B and TM1088A dimers is measured as ~80° (Fig 6D).

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.


Related in: MedlinePlus