TCDB is operated by the Saier Lab Bioinformatics Group

1.B.35 The Oligogalacturonate-specific Porin (KdgM) Family

Gram-negative enteric bacteria (species of Yersinia, Salmonella, Vibrio and Escherichia) possess homologues of the functionally characterized oligogalacturonate-specific porin, KdgM, of Erwinia chrysanthemi. These proteins comprise the current KdgM family. E. chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. The major outer membrane protein, KdgM, whose synthesis is strongly induced in the presence of pectic derivatives, was characterized (Blot et al., 2002). Analysis of transcriptional fusions showed that kdgM expression is controlled by the general repressor of pectinolytic genes, KdgR, by the repressor of hexuronate catabolism genes, ExuR, by the pectinase gene repressor, PecS, and by catabolite repression via the CRP transcriptional activator. A kdgM mutant is unable to grow on oligogalacturonides longer than trimers and is affected as regards its virulence. Electrophysiological experiments with planar bilayers showed that KdgM behaves like a voltage-dependent porin which is slightly selective for anions and which exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric. KdgM is homologous to NanC (see below) and members of the OmpG family (TC #1.B.21) (Blot et al., 2002; Condemine et al., 2005). KdgM shows limited sequence similarities with portions of invasins and intimins (TC# 1.B.54).

E. chysanthemi (renamed Dickeya dadantii) has two oligogalacturonate outer membrane porins, KdgM and KdgN. Both have mild anionic selectivity. They overlap functionally and are controlled by the same five transcription factors. However, two of these factors act on the kdgM and kdgN genes in opposite directions (Condemine G, 2007) suggesting that they function under different conditions. The structures of KdgM, KdgN and NanC have been solved (7Å resolution) by electron microscopy (Signorell et al. 2007). The predicted transmembrane beta-barrels have high similarity in the arrangement of the putative beta-strands and the loops, but do not match those of OmpG, a related protein porin (see OmpG superfamily) whose structure has been solved.

A crystal structure (3.3 Å resolution) is available for NanC (1.B.35.2.1) (Wirth et al., 2009). It forms a 28 Å high 12 stranded β barrel like the autotransporter, NalP. The pore is lined by basic residues (conserved in other KdgM family members) allowing diffusion of acidic oligosaccharides (Wirth et al., 2009).

The KdgM family is distantly related to members of the OmpG family (1.B.21).

References associated with 1.B.35 family:

Blot, N., C. Berrier, N. Hugouvieux-Cotte-Pattat, A. Ghazi and G. Condemine. (2002). The oligogalacturonate specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family. J. Biol. Chem. 277: 7936-7944. 11773048
Condemine G., Ghazi A. (2007). Differential regulation of two oligogalacturonate outer membrane channels, KdgN and KdgM, of Dickeya dadantii (Erwinia chrysanthemi). J Bacteriol. 189: 5955-5962. 17573480
Condemine, G., C. Berrier, J. Plumbridge, and A. Ghazi. (2005). Function and expression of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli. J. Bacteriol. 187: 1959-1965. 15743943
Freeman, T.C., Jr, S.J. Landry, and W.C. Wimley. (2011). The prediction and characterization of YshA, an unknown outer-membrane protein from Salmonella typhimurium. Biochim. Biophys. Acta. 1808: 287-297. 20863811
García-Sureda, L., A. Doménech-Sánchez, M. Barbier, C. Juan, J. Gascó, and S. Albertí. (2011). OmpK26, a novel porin associated with carbapenem resistance in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 55: 4742-4747. 21807980
Giri, J., J.M. Tang, C. Wirth, C.M. Peneff, and B. Eisenberg. (2012). Single-channel measurements of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli. Eur Biophys. J. 41: 259-271. 22246445
Hutter, C.A., R. Lehner, C.h. Wirth, G. Condemine, C. Peneff, and T. Schirmer. (2014). Structure of the oligogalacturonate-specific KdgM porin. Acta Crystallogr D Biol Crystallogr 70: 1770-1778. 24914987
Signorell, G.A., M. Chami, G. Condemine, A.D. Schenk, A. Philippsen, A. Engel, and H.W. Remigy. (2007). Projection maps of three members of the KdgM outer membrane protein family. J Struct Biol 160: 395-403. 17919922
Wargacki, A.J., E. Leonard, M.N. Win, D.D. Regitsky, C.N. Santos, P.B. Kim, S.R. Cooper, R.M. Raisner, A. Herman, A.B. Sivitz, A. Lakshmanaswamy, Y. Kashiyama, D. Baker, and Y. Yoshikuni. (2012). An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335: 308-313. 22267807
Wirth C., Condemine G., Boiteux C., Berneche S., Schirmer T. and Peneff CM. (2009). NanC crystal structure, a model for outer-membrane channels of the acidic sugar-specific KdgM porin family. J Mol Biol. 394(4):718-31. 19796645