1.B.26 The Cyclodextrin Porin (CDP) Family

A single functionally characterized protein, the CymA cyclodextrin porin of Klebsiella oxytoca, comprises the CDP family. Cyclodextrins (CDs) are cylindrically shaped oligosaccharides made up of six (α-CD), seven (β-CD) or eight (γ-CD) glucosyl residues. The hydroxyl groups border the outside of the ring forming water soluble molecules with hydrophobic cavities. They are formed from starch by microorganisms in reactions catalyzed by cyclodextrin glucanotransferases which are secreted into the medium where they make the cyclodextrins that can be taken up and used as sources of carbon and energy. They cross the outer bacterial membrane via the CD porin, CymA of K. oxytoca. This porin can also transport linear maltodextrins (Pajatsch et al., 1999).

CymA is not recognizably homologous to other characterized porins, but it resembles them in that (1) it is rich in antiparallel β-sheets, (2) it is a component of the outer membrane, and (3) it is processed from a precursor having a signal peptide. CymA, reconstituted in lipid bilayers, conducts ions blocked by the presence of cyclodextrins (CDs) (K= 28 μM) Cyclodextrins bind with high stability, but straight chained (linear) maltooligosaccharides also bind (Orlik et al., 2003). It forms a homotetramer with a central pore, and therefore lacks the typical trimeric structure of most porins. The CDP family is distantly related to the OmpG and OmpL porins in the OmpG family (1.B.21).

The generalized transport reaction catalyzed by CymA is:

Cyclodextrin (out) or linear maltodextrin (out) cyclodextrin (in) or linear maltodextrin (in)

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



Bhamidimarri, S.P., J.D. Prajapati, B. van den Berg, M. Winterhalter, and U. Kleinekathöfer. (2016). Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example. Biophys. J. 110: 600-611.

Orlik, F., C. Andersen, C. Danelon, M. Winterhalter, M. Pajatsch, A. Böck, and R. Benz. (2003). CymA of Klebsiella oxytoca outer membrane: binding of cyclodextrins and study of the current noise of the open channel. Biophys. J. 85: 876-885.

Pajatsch, M., C. Anderson, A. Mathes, A. Böck, R. Benz and H. Engelhardt. (1999). Properties of a cyclodextrin-specific, unusual porin from Klebsiella oxytoca. J. Biol. Chem. 274: 25159-25166.


TC#NameOrganismal TypeExample

Cyclodextrin (high affinity)/linear malto-oligosaccharide (low affinity) porin, CymA (Orlik et al. 2003).  Electroosmosis influences the transport efficiency of cyclodextrins through the CymA pore (Bhamidimarri et al. 2016).

Gram-negative bacteria

CymA of Klebsiella oxytoca


Putative porin, CymA


Putative porin of Vibrio cholerae


TC#NameOrganismal TypeExample

Putative porin of 331 aas


Putative porin of Yersinia pestis


Putative porin of 392 aas


Putative porin of Rahnella aquatilis