FimD Usher Family Paralogs


The FimD family of eleven genes are predicted to be outer membrane fimbrial subunit export usher proteins involved in export and assembly of type 1 fimbrial subunits. This paralogous family includes three apparent pseudogenes. YqiG and YfcU are full length pseudogene reconstructions in which IS2I and stop codon 579, respectively, have been hypothetically reverted. The pseudogene ydeT encodes a C-terminal fragment that has been omitted from the EcoFam alignment and family tree. PapC is the most well-studied member fo this family, also called the The Outer Membrane Fimbrial Usher Porin (FUP) Family in the Transporter Classification Database TCDB, which uses the Transporter Classification (TC) system and classifies the FimD paralogs as TC 1.B.11. Many of the FimD paralogs are located in operons with pilin (FimA) and chaperone (FimC) paralogs, indicating cognate chaperone partners and substrates for the various ushers. The predicted ECP usher protein EcpC is distantly related to FimD and has been included in this topic but left out of the multiple alignment.


EcoFam Multiple Alignment of the FimD Outer Membrane Usher Family Paralogs:
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EcoFam Paralog Tree of the FimD Family:
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The multiple alignment was created using the EBI Muscle server. The multiple alignment figure was produced using the ESPript server at the Universite de Lyon, France.The unrooted tree diagrams are drawn using the Phylodendron server at Indiana University.

The crystal structure of a complex of the FimD N-terminal periplasmic domain (46-170), the FimC periplasmic chaperone, and the C-terminal pilin domain of FimH (158-279 aa): PDB 1ZE3 (Nishiyama, 2005). Two NMR structures of FimD are also available: PDB 1ZDV and PDB 1ZDX.

The crystal structure of the pilus elongation complex in which the tip complex assembly composed of FimC, FimF, FimG and FimH passes through the usher porin FimD has been determined: PDB 4J3O depicted in Figure 1 (Geibel, 2013).

FimD forms outer membrane pores for the extrusion of fimbrial (pilin) subunits as part of the FimCD chaperone-usher pilin transport system. After traversing the inner membrane via the Sec translocon, pilin subunits (FimA,F,G,H) associate with the FimC periplasmic chaperone. The FimC chaperone allows the pilin subunits to fold but not assemble. The periplasmic N-terminal domain of FimD initially recognizes the chaperone(FimC)-pilin complexes. Then, at the FimD usher OM pore, the FimC-pilin-FimD interaction acts by donor strand complementation (DCE) to utilize chaperone-pilin complex dissociation to drive fiber assembly and export.

Some studies utilize the homologous PapC usher, which forms twin pores. FimD is the only one of the E. coli K-12 paralogs that has been functionally characterized as an usher. The signal cleavage site for FimD has been proven to be after residue 45. HtrE has been reported to be a heat shock protein required for high temperature growth, and has a 29 aa signal peptide. Cleavage sites for the other FimD paralogs are predicted using SignalP. YraJ lacks the N-terminal conserved Cys pair, but has the C-terminal Cys pair. For additional usher family information see Pfam PF00577, PROSITE PS01151, NCBI COG3188 and TCDB 1.B.11.