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Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate

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ABSTRACT

Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters.

No MeSH data available.


Modeling of YkoEDC Complex(A) Theoretical model of YkoEDC complex. YkoE is shown in orange, the homology model of YkoC in gray, and the homology model of YkoD in aquamarine.(B) Theoretical model of YkoEC complex. YkoE is shown in orange, the homology model of YkoC colored according to conservation scores (cyan, variable; burgundy, conserved), the most conserved parts of YkoC are the helices CH2 and CH3, which are probably involved in interactions with YkoE and YkoD. An insertion and deletion in YkoC compared with EcfT could potentially result in some mechanistic differences between these T components. In YkoC, the loop connecting helix CH3 and transmembrane helix H5 is longer, and the hinge region between CH1 and CH2 is much shorter compared with the group II Ecf T component. The similarities in the pairwise alignments used to build the homology models are: YkoC and EcfT, 28%; YkoD N-terminal domain and EcfA2, 37%; YkoD C-terminal domain and EcfA1, 33% sequence identity.
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fig7: Modeling of YkoEDC Complex(A) Theoretical model of YkoEDC complex. YkoE is shown in orange, the homology model of YkoC in gray, and the homology model of YkoD in aquamarine.(B) Theoretical model of YkoEC complex. YkoE is shown in orange, the homology model of YkoC colored according to conservation scores (cyan, variable; burgundy, conserved), the most conserved parts of YkoC are the helices CH2 and CH3, which are probably involved in interactions with YkoE and YkoD. An insertion and deletion in YkoC compared with EcfT could potentially result in some mechanistic differences between these T components. In YkoC, the loop connecting helix CH3 and transmembrane helix H5 is longer, and the hinge region between CH1 and CH2 is much shorter compared with the group II Ecf T component. The similarities in the pairwise alignments used to build the homology models are: YkoC and EcfT, 28%; YkoD N-terminal domain and EcfA2, 37%; YkoD C-terminal domain and EcfA1, 33% sequence identity.

Mentions: None of the features characteristic for the group II transporters are present in YkoE, and this likely accounts for why YkoE does not associate with group II ECF modules (Figure 2C). Instead of the ΦxxxA motif, YkoE contains a semi-conserved S/AxxxI/VV motif located at the equivalent position on helix H1. This motif probably interacts with the CH2 helix of its T component YkoC. We modeled the YkoE-YkoC complex using a YkoC homology model and the EcfS(PanT)-EcfT complex as a template. The main interactions between YkoE and YkoC probably involve a large hydrophobic interface defined by helix H1 and the groove between H1 and H6 of YkoE and the highly conserved coupling helices CH2 and CH3 of YkoC. We speculate that the interaction between helix H1 and CH2 in the YkoE-YkoC complex is mediated by a hydrophobic/shape complementarity interaction between the branched amino acid I/V on the YkoE helix H1 and a highly conserved Gly144 on the YkoC helix CH2 (Figure 7). The lack of strong sequence conservation in helix H1 is probably due to the uniqueness of the YkoE-YkoC interface that was shaped during speciation through the co-evolution of the two binding partners.


Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate
Modeling of YkoEDC Complex(A) Theoretical model of YkoEDC complex. YkoE is shown in orange, the homology model of YkoC in gray, and the homology model of YkoD in aquamarine.(B) Theoretical model of YkoEC complex. YkoE is shown in orange, the homology model of YkoC colored according to conservation scores (cyan, variable; burgundy, conserved), the most conserved parts of YkoC are the helices CH2 and CH3, which are probably involved in interactions with YkoE and YkoD. An insertion and deletion in YkoC compared with EcfT could potentially result in some mechanistic differences between these T components. In YkoC, the loop connecting helix CH3 and transmembrane helix H5 is longer, and the hinge region between CH1 and CH2 is much shorter compared with the group II Ecf T component. The similarities in the pairwise alignments used to build the homology models are: YkoC and EcfT, 28%; YkoD N-terminal domain and EcfA2, 37%; YkoD C-terminal domain and EcfA1, 33% sequence identity.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037267&req=5

fig7: Modeling of YkoEDC Complex(A) Theoretical model of YkoEDC complex. YkoE is shown in orange, the homology model of YkoC in gray, and the homology model of YkoD in aquamarine.(B) Theoretical model of YkoEC complex. YkoE is shown in orange, the homology model of YkoC colored according to conservation scores (cyan, variable; burgundy, conserved), the most conserved parts of YkoC are the helices CH2 and CH3, which are probably involved in interactions with YkoE and YkoD. An insertion and deletion in YkoC compared with EcfT could potentially result in some mechanistic differences between these T components. In YkoC, the loop connecting helix CH3 and transmembrane helix H5 is longer, and the hinge region between CH1 and CH2 is much shorter compared with the group II Ecf T component. The similarities in the pairwise alignments used to build the homology models are: YkoC and EcfT, 28%; YkoD N-terminal domain and EcfA2, 37%; YkoD C-terminal domain and EcfA1, 33% sequence identity.
Mentions: None of the features characteristic for the group II transporters are present in YkoE, and this likely accounts for why YkoE does not associate with group II ECF modules (Figure 2C). Instead of the ΦxxxA motif, YkoE contains a semi-conserved S/AxxxI/VV motif located at the equivalent position on helix H1. This motif probably interacts with the CH2 helix of its T component YkoC. We modeled the YkoE-YkoC complex using a YkoC homology model and the EcfS(PanT)-EcfT complex as a template. The main interactions between YkoE and YkoC probably involve a large hydrophobic interface defined by helix H1 and the groove between H1 and H6 of YkoE and the highly conserved coupling helices CH2 and CH3 of YkoC. We speculate that the interaction between helix H1 and CH2 in the YkoE-YkoC complex is mediated by a hydrophobic/shape complementarity interaction between the branched amino acid I/V on the YkoE helix H1 and a highly conserved Gly144 on the YkoC helix CH2 (Figure 7). The lack of strong sequence conservation in helix H1 is probably due to the uniqueness of the YkoE-YkoC interface that was shaped during speciation through the co-evolution of the two binding partners.

View Article: PubMed Central - PubMed

ABSTRACT

Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters.

No MeSH data available.