3gbh

Protein Summary

The gene SE1966 (refseq accessin number NP_765521.1) belongs to the Nitroreductase, PF00881, Pfam A group. This Pfam group is represented by 71 structures in the Protein Data Bank.

The structure of NP_765521.1  is a member of the Nitroreductase-like family from Staphylococcus epidermidids strain ATCC 12228 . This strain is a non-biofilm-forming, non-infection associated strain used for detection of residual antibiotics in food products.  Nitroreductases  typically require NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.  The structure described here was determined at a resolution of 2.0 Angstroms using single wavelength anomalous dispersion methods (SAD).

 Shown here is a ribbon representation of the structure of the dimer of NP_765521.1 color coded with the N-terminal region in blue and the C-terminal region in red. An FMN, tightly bound to each monomer is shown in the red sticks. The crystal structure indicates that the dimer represented here is a significant oligomerization state. Recently refined JCSG structures similar to NP_765521.1 also include YP_001089721.1 from Clostridium difficile 630 and NP_904626.1 from Porphyromonas gingivalis w83. The refined coordinates for NP_76552.1 were used as a template to search for structurally-similar proteins using the fastSCOP evolutionary classification server. This serarch shows that NP_766552.1 most likely belongs to the NADH oxidase/flavin reductase SCOP family. An NCBI VAST search shows several targets in the Protein Data Bank that show a similar structure. Among these targets are PDB ID 2B67 (Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4, rmsd 1.85 Angstroms, seq id 25%), PDB ID 1NOX (NADH Oxidase from Thermus thermophilus; rmsd 1.62 Angstroms, 25% sequence id), PDB ID 2HAY ( The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS; ), PDB ID 1ICU (the structure of E.coli Nitroreductase Complex with Nicotinic Acid), and PDB ID 3BEM ( Crystal Structure Of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis At 1.65 A Resolution).

Shown below is a representation of the structure of NP_765521.1 in the vicinity of the putative active site.  One monomer in the dimer is shown in yellow ribbons and the symmetry-related dimer is shown in blue ribbons. A bound FNM (red sticks) is also shown superimposed on 2fo-fc electron density. An unknown ligand (represented by red spheres and its corresponding electron density) is situated near one face of the bound FMN cofactor.

Ligand Summary