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).
This family belongs to the Outer Membrane Pore-forming Protein I (OMPP-I) Superfamily .
References:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Examples:
TC#	Name	Organismal Type	Example
1.B.35.1.1	The oligogalacturonate-specific porin, KdgM. The 3-D structure is known at 1.9 Å resolution (Hutter et al. 2014). KdgM folds into a 12-stranded antiparallel beta-barrel with a circular cross-section defining a transmembrane pore with a minimal radius of 3.1 Å. Most loops that face the cell exterior in vivo are disordered but nevertheless mediate contact between densely packed membrane-like layers in the crystal. The channel is lined by two tracks of arginine residues facing each other across the pore, a feature that is conserved within the KdgM family and is likely to facilitate the diffusion of acidic oligosaccharides (Hutter et al. 2014).	Gram-negative γ-proteobacteria	KdgM of Erwinia chrysanthemi (Dickeya dadantii)

1.B.35.1.2	The second oligogalacturonate-specific Gram negative porin, KdgN (60% identical to KdgM; 1.B.35.1.1) (Condemine and Ghazi, 2007).	Gram-negative γ-proteobacteria	*KdgN of Dickeya dadantii* (Erwinia carotovora) (Q6D4T8)**

1.B.35.1.3	*Alginate-oligosaccharide-specific porin, KdgM (Wargacki et al., 2012).*	Gram-negative bacteria	*KdgM of Vibrio speldidus* (A3UR43)**

1.B.35.1.4	*Alginate-oligosaccharide-specific porin, KdgN (Wargacki et al., 2012)*	Gram-negative bacteria	*KdgN of Vibrio splendidus* (A3UR51)**

1.B.35.1.5	KdgM homologue of 227 aas	Proteobacteria	KdgM homologue of Enterobacter cloacae

1.B.35.1.6	Putative KdgM porin of 224 aas	Proteobacteria	KdgM porin of Serratia marcescens

1.B.35.1.7	*OmpK26 porin (YjhA) of 231 aas; associated with carbapenem resistance (García-Sureda et al.* 2011).**	Proteobacteria	OmpK26 of Klebsiella pneumoniae

Examples:
TC#	Name	Organismal Type	Example
1.B.35.2.1	The N-acetylneuraminic acid-inducible, anion selective porin, NanC (Condemine et al., 2005). A crystal structure (3.3 Å resolution) is available (2WJQ; 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). Single channels of NanC at pH 7.0 have: (1) conductance 100 to 800 pS in 100 mM: KCl to 3 M: KCl), (2) anion over cation selectivity, and (3) two forms of voltage-dependent gating (channel closures above 200 mV). Phosphate interferes with channel conductance (Giri et al. 2012).	Gram-negative γ-proteobacteria	*NanC (YjhA) of E. coli* (P69856)**

1.B.35.2.2	OmpL porin. Nearly identical to Salmonella typhimurium YshA which appears to be a 10 β-stranded transmembrane β-barrel which forms a pore with a radius of 0.7nm (Freeman et al., 2011). May be an oligogalacturonate-specific porin (Shevchik and Hugouvieux-Cotte-Pattat, 2003).	Gram-negative bacteria	OmpL of E. coli

1.B.35.2.3	Putative porin of 233 aas	Proteobacteria	Putative porin of Owenweeksia hongkongensis

1.B.35.2.4	Uncharacterized protein of 218 aas.		UP of Zixibacteria bacterium SM1_73

Examples:
TC#	Name	Organismal Type	Example
1.B.35.3.1	Putative porin of 230 aas	Proteobacteria	Putative porin of Vibrio parahaemolyticus

1.B.35.3.2	Putative porin of 236 aas	Proteobacteria	Putative porin of Psychromonas sp.

Examples:
TC#	Name	Organismal Type	Example
1.B.35.4.1	Putative porin of 263 aas	Proteobacteria	Putative porin of Photobacterium profundum

1.B.35.4.2	Putative porin of 282 aas	Proteobacteria	Putative porin of Photobacterium profundum

1.B.35.4.3	Putative porin of 267 aas	Proteobacteria	Porin of Vibrio orientalis