Protein Name

Outer membrane porin D2 (OprD)


Pseudomonas aeruginos

Biological Context

Pseudomonas aeruginosa is a Gram-negative bacterium observed in ubiquitous environment. This bacterium is noted for its ability to cause the opportunistic infections in immune-compromised patient and for its high resistance to various antibiotics. Therefore its infections are difficult to treat and known as a major clinical problem. The high drug-resistance of this bacteria is partly due to its low outer-membrane permeability. In Gram-negative bacteria such as Escherichia coli, most small water-soluble molecules(including antibiotics) enter the intracellular by diffusion through the channels of nonspecific porins located in the outer-membrane (Fig.1). However, some Gram-negative bacteria such as P. aeruginosa possess substrate-specific porins instead of nonspecific porin. Specific porins are different from nonspecific porins in that they allow for the passive diffusion of specific substrates efficiently. For this reason, foreign substances such as antibiotics are difficult to enter the cell. OprD family proteins are substrate-specific porin, and have a function of mediating the specific uptake of basic amino acids. Despite the importance of the OprD family for the functioning of many Gram-negative bacteria, the structures have not been solved for any member of this family. The authors have determined the crystal structure of P. aeruginosa OprD which is prototype of the OprD family. The structural information may show hints to overcome the P. aeruginosa infections.

(Fig.1) Double membranes of Gram-negative bacteria
The outer membrane of Gram-negative bacteria serves as a filter
for hydrophilic substances, and protects cells. Nutrients
molecular such as amino acids or glucose enter the intracellular
through channels of porins located in the outer-membrane.
    • Other specific porin
      • LamB (maltose)
      • ScrY (sucrose)
      • OprP(phosphate)
      • OprO(polyphosphate )
      • OprB(glucose)

Structure Description


OprD crystal structure as a monomeric forms 18-stranded β-barrel (Fig.2). OprD may exist as a labile trimer within the outer membrane. Two long loops, L3 and L7, fold inward to the interior of barrel wall. A very narrow, roughly circular pore (~5.5 A ° in diameter) is formed between the two loops and two residues (Arg391 and Arg410) from barrel wall (Fig.3). Several residues in this region are well conserved in other members of OprD family. This indicates that these residues are important for substrate selection in the OprD family.

(Fig.2) Structure of OprD monomer
(Fig.3) Residues around the pore

The size of the pore was enlarged as a result of removal of the L3. This indicate that L3 contributes to substrate selectivity by narrowing the pore size.

(Fig.4) Comparison fo wild type and L3 mutant

Protein Data Bank (PDB)



Biswas, S. Mohammad, M.M. Patel, D.R. Movileanu, L. van den Berg, B.; "Structural insight into OprD substrate specificity."; Nat.Struct.Mol.Biol.; (2007) 14:1108-1109 PubMed:17952093.


author: Jun-ichi Ito

Japanese version:PDB:2ODJ