3ek3

Protein Summary

An obligate anaerobe, Bacteroides fragilis is usually a commensal organism, forming a large component of the normal human gut microbiota. However it is also an important opportunistic pathogen, with the potential to severly limit the success of gastro-intestinal surgery. YP_211706.1 from this medically-important organisim has been determined by MAD to a resolution of 1.7 Angstroms and refined to an (Rfree=18.3%)

 The Figure above shows a ribbon representation of the structure of YP_211706.1. The polypeptide ribbon is color-coded with the N-terminal end in blue and the C-terminal end in red. The x-ray structure shows the presence of a bound Flavin Mononucleotide (FMN) cofactor shown with red sticks. The FMN binds on one side of a beta sheet . The other side of the sheet is flanked by alpha-helices. From residue 167 to the C-terminal end, the polypeptide chain forms an extended beta strand. This extended beta stand interacts with a monomer related by crystallographic symmetry in the C222(1) crystal lattice of the protein crystal.

The amino acid sequence of YP_211706.1 and the corresponding secondary structure topology.

The PISA protein assembly prediction server indicates that the biologically significant oligomerization state in solution for  YP_211706.1 is the dimer.

Shown to the left is a ribbon representation of the dimer with the indivifual monomers of the dimer shown in blue and green respectively. The extended beta-strand at the C-terminal end of each monomer interacts with the symmetry related monomer to form a five strand beta sheet.The FMN cofactor on each subunit is shown in red. Immediately adjacent to and stacked against the side of the FMN ring facing the solvent is crystallographic evidence for the binding of a biologically-relevant ligand. Extra electron density at this position was modeled as an unknown ligand (UNL) in the structure (grey dots).

An InterPro scan reveals the sequence motif of  YP_211706.1 belongs to the nitroreductase family that uses FMN as a cofactor (PF00881). This family is involved in the reduction of nitrogen containing compounds. Members of this family utilise FMN as a cofactor and are often found to be homodimers. Possible characteristics include Oxygen-insensitive NAD(P)H nitroreductase (FMN-dependent nitroreductase) (Dihydropteridine reductase) and NADH dehydrogenase. A number of the proteins are described as oxidoreductases. They are primarily found in bacterial lineages though a number of eukaryotic homologs have been identified: Caenorhabditis elegans , Drosophila melanogaster , mouse and human . This protein is not found in photosynthetic eukaryotes. The sequences containing this entry in photosynthetic organisms are possible false positives.

  An EBI SSM search of the Protein Data Bank using the coordinates of YP_211706.1 as a search model shows several protein structures have been determined that are similar to the structure of YP_211706.1. The table below lists the structurally-similar proteins.

Ligand Summary

Among the most significant feature revealed by the structure determination, is the presence of a bound FMN cofactor. Shown below is a diagram of the structure in dimer in the vicinity of the FMN binding site. Most of the close range interactions (hydrogen bonds-black dashes) form between FMN and one of the monomers in the dimer (green region in the Figure below). However,  sidechain and mainchain atoms from the symmetry related monomer (blue region in Figure below) are within Van der Waals contact distance. In addition, an MPD molecule (from the crystallization buffer) also is within hydrogen bonding contact distance from the phosphate moiety on the FMN cofactor.