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The Oligogalacturonate-specific porin protein (KdgM) Family [Function: Specific diffusion channels] Seed alignment | Full alignment | Pfam page | Pfam Wiki page | TC-DB page

This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM from Erwinia chrysanthemi. This phytopathogenic Gram-negative bacterium 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. KdgM is a Major Outer Membrane Protein (MOMP), whose synthesis is induced in the presence of the pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. The family members seem to be monomeric, while the determined 3D structure of NanC porin suggests that they possess a 12-stranded ß-barrel, with rather short extracellular loops and a larger one that restricts the size of the pore. An outer membrane porin, KdgM, is indispensable for the uptake of acidic oligosaccharides. KdgM is folded into a regular 12-stranded antiparallel ß-barrel with a circular cross-section defining a transmembrane pore with a minimal radius of 3.1?Å.


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Literature references


Structure of the oligogalacturonate-specific KdgM porin
Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1770-8. doi: 10.1107/S1399004714007147. Epub 2014 May 30.
PMID: 24914987

The free energy landscape of dimerization of a membrane protein, NanC
PLoS Comput Biol. 2014 Jan;10(1):e1003417. doi: 10.1371/journal.pcbi.1003417. Epub 2014 Jan 9.
PMID: 24415929

Simulation of ion transport through an N-acetylneuraminic acid-inducible membrane channel: from understanding to engineering
J Phys Chem B. 2013 Dec 19;117(50):15966-75. doi: 10.1021/jp408495v. Epub 2013 Nov 14.
PMID: 24161028

Ion permeation in the NanC porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations
J Phys Chem B. 2013 Oct 31;117(43):13534-42. doi: 10.1021/jp4081838. Epub 2013 Oct 22.
PMID: 24147565

Single-channel measurements of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli
Eur Biophys J. 2012 Mar;41(3):259-71. doi: 10.1007/s00249-011-0781-5. Epub 2012 Jan 13.
PMID: 22246445

Loss of elongation factor P disrupts bacterial outer membrane integrity
J Bacteriol. 2012 Jan;194(2):413-25. doi: 10.1128/JB.05864-11. Epub 2011 Nov 11.
PMID: 22081389

OmpK26, a novel porin associated with carbapenem resistance in Klebsiella pneumoniae
Antimicrob Agents Chemother. 2011 Oct;55(10):4742-7. doi: 10.1128/AAC.00309-11. Epub 2011 Aug 1.
PMID: 21807980

NanC crystal structure, a model for outer-membrane channels of the acidic sugar-specific KdgM porin family
J Mol Biol. 2009 Dec 11;394(4):718-31. doi: 10.1016/j.jmb.2009.09.054. Epub 2009 Sep 29.
PMID: 19796645

Projection maps of three members of the KdgM outer membrane protein family
J Struct Biol. 2007 Dec;160(3):395-403. doi: 10.1016/j.jsb.2007.08.007. Epub 2007 Aug 23.
PMID: 17919922

Function and expression of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli
J Bacteriol. 2005 Mar;187(6):1959-65. doi: 10.1128/JB.187.6.1959-1965.2005.
PMID: 15743943

Topology of the Erwinia chrysanthemi oligogalacturonate porin KdgM
Biochem J. 2003 Jun 1;372(Pt 2):329-34. doi: 10.1042/BJ20030027.
PMID: 12603200

The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family
J Biol Chem. 2002 Mar 8;277(10):7936-44. doi: 10.1074/jbc.M109193200. Epub 2001 Dec 28.
PMID: 11773048

Proteins in this family with 3D-structure
View Entry
Description
Organism
Length
# strands
Outer membrane protein OmpK
Escherichia coli (strain K12)
238
12
Hemoglobin binding protein A
Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937))
236
12


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