1.B.7 The Rhodobacter PorCa Porin (RPP) Family

The Rhodobacter PorCa Protein, the only well characterized member of the RPP family, was the first porin to yield its three-dimensional structure by X-ray crystallography. It has a 16-stranded β-barrel structure similar to that of the members of the GBP (TC #1.B.1) family. Paupit et al. (1991) presented crystal structures of phosphoporin (PhoE; TC# 1.B.1.1.2), maltoporin (1.B.3.1.1; LamB) and Matrixporin (OmpF), all of E. coli, and found these have 3-d folds similar to that of the Rhodobacter porin, PorCa. It was not determined if this similarity is due to divergent evolution from a common ancestor or covergent evolution from dissimilar precursors. However, we have been able to demonstrate homology between members of families 1.B.1 and 1.B.7 using statistical means (M. Saier, unpublished results).



This family belongs to the Outer Membrane Pore-forming Protein (OMPP) Superfamily I.

 

References:

Burdman, S., R. De Mot, J. Vanderleyden, Y. Okon, and E. Jurkevitch. (2000). Identification and characterization of the omaA gene encoding the major outer membrane protein of Azospirillum brasilense. DNA Seq 11: 225-237.

Jeanteur, D., J.H. Lakey and F. Pattus (1991). The bacterial porin superfamily: sequence alignment and structure prediction. Mol. Microbiol. 5: 2153-2164.

Jeanteur, D., J.H. Lakey and F. Pattus (1994). The porin superfamily: diversity and common features. In: Bacterial Cell Wall. Edited by Ghuysen, J.M., Hakenbeck, R. Elsevier, Amsterdam, pp. 363-380.

Kreusch, A. and G.E. Schultz (1994). Refined structure of the porin from Rhodopseudomonas blastica and comparison with the porin from Rhodobacter capsulatus. J. Mol. Biol. 243: 891-905.

Moumène, A., I. Marcelino, M. Ventosa, O. Gros, T. Lefrançois, N. Vachiéry, D.F. Meyer, and A.V. Coelho. (2015). Proteomic Profiling of the Outer Membrane Fraction of the Obligate Intracellular Bacterial Pathogen Ehrlichia ruminantium. PLoS One 10: e0116758.

Nikaido, H. (1992). Porins and specific channels of bacterial outer membranes. Mol. Microbiol. 6: 435-442.

Pauptit, R.A., T. Schirmer, J.N. Jansonius, J.P. Rosenbusch, M.W. Parker, A.D. Tucker, D. Tsernoglou, M.S. Weiss, and G.E. Schultz. (1991). A common channel-forming motif in evolutionarily distant porins. J Struct Biol 107: 136-145.

Saxena, K., O.M. Richter, B. Ludwig, and R. Benz. (1997). Molecular cloning and functional characterization of the Paracoccus denitrificans porin. Eur J Biochem 245: 300-306.

Schiltz, E., A. Kreusch, U. Nestel and G.E. Schulz (1991). Primary structure of porin from Rhodobacter capsulatus. Eur. J. Biochem. 199: 587-594.

Schulz, G.E. (1996). Porins: general to specific, native to engineered passive pores. Curr. Opin. Struc. Biol. 6: 485-490.

Weiss, M.S., T. Wacker, J. Weckesser, W. Welte and G.E. Schulz (1990). The three-dimensional structure of porin from Rhodobacter capsulatus at 3 Å resolution. FEBS Lett. 267: 268-272.

Examples:

TC#NameOrganismal TypeExample
1.B.7.1.1

PorCa (B10) porin.  The 3-d structure is known (PDB ID 2POR).

Bacteria PorCa porin of Rhodobacter capsulatus
 
1.B.7.1.2

Paracoccus ion non-selective porin with 16 putative beta-strands, PorG (Saxena et al. 1997).

Bacteria

Porin of Paracoccus denitrificans

 
1.B.7.1.3

PorI (OpmA) porin.  Forms channels that allow the passive diffusion of small hydrophilic solutes up to an exclusion limit of about 600 Da.  The 3-d structure is known (PDB ID 1PRN).

Bacteria

PorI porin of Rhodobacter (Rhodopseudomonas) blastica

 
1.B.7.1.4

OmaA major-porin (Burdman et al., 2000).

Gram-negative bacteria

OmaA of Azospirillum brasilense (Q9F9L3)

 
1.B.7.1.5

Porin 41 (Por41) (Kleeberg, V., Neumann, U., Schultz, G.E. and Weckesser, J., unpublished)

Gram-negative bacteria

Por41 of Rhodospirillum rubrum (Q9K556)

 
1.B.7.1.6Outer membrane porin

Proteobacteria

SPO3430 of Silicibacter pomeroyi
 
1.B.7.1.7

Putative porin of 332 aas

Proteobacteria

Putative porin of Rhodopseudomonas sphaeroides

 
1.B.7.1.8

Porin of 385 aas (Moumène et al. 2015).

Proteobacteria

Porin of Ehrlichia ruminantium

 
Examples:

TC#NameOrganismal TypeExample