3gfa

Protein Summary

Gene CD3205 translates into the YP_001089721 protein encoded by Clostridium difficile 630, a ubiquitous microbe found in both human and animal feces. The bacterium is especially prevalent  in in hospital environments. Under certain circumstances, this bacterium is pathogenic. The amino acid sequence for this target belongs to the Nitroreductase PF00881 Pfam Group.

The 3gfa structure belongs to the alpha + beta class and reveals a FMN-dependent nitroreductase like fold, inside the SCOP NADH oxidase/flavin reductase family. Top DALI hits are with the nitroreducatse PDB:3e39 (Z=20), PDB:2i7h (Z=19), and PDB:1ywq (Z=19). Two additional JCSG targets that are structurally related to 3gfa include PDB:3eo8 (Z=21, topsan) and PDB:3eof  (Z=17, topsan). PDB ID 3eo8 shares several important features with 3gfa. First, both targets are from the same microcobe, Clostridium difficile 630. Second, both targets contain a tightly bound flavin mononucletide (FMN) cofactor. Third, both structures (3fga and 3eo8) show chloride anions bound at the active site near the FMN, and the presence of this negtaively-charged anion suggests a role for these two proteins in oxygen reduction.

The x-ray crystal structure reported here, 3gfa, was determined by selenoMet-based multiwavelength anomalous dispersion at a resolution of 1.35 Angstroms. Shown below is a ribbon representation of the crystal structure of 3gfa. The polypeptide backbone is color-coded rainbow with the N-terminus in blue and the C-terminal region in red. An FMN prosthetic group is bound to the target (red sticks). The C-terminal extension of the monomer interacts with a beta-strand on a symmetry-related monomer.

Comparison with the structure of related proteins such as PDB ID 3eo8 and PDB ID 3eof suggest that the biologically significant oligomerization state of 3gfa is a dimer. Shown below it is a ribbon representation of the structure of the dimer with the individual monomers depicted in green and blue. The bound FMN cofactors are shown in red. The monomers are related by a two-fold non crystallographic dyad axis. The C-terminal end of each monomer contributes a beta strand to a symmetry-related monomer in the dimer to form a five-stranded beta sheet. In addition, each FMN cofactor interacts with residues from both monomers within the dimer.

A search of the Protein Data Bank for entries structurally-related to 3gfa was performed using the EBI Secondary Structure Match Server. The results are:

Hit	Z-score	No.   SSE	RMSD   (Å)	Seq.   id	PDB   entry	Name
1	10.0	12	1.19	33.1%	3e39	Crystal structure of putative nitroreductase in complex with fmn (yp_387283.1) from desulfovibrio desulfuricans g20 at 1.70 a resolution
2	7.6	11	1.57	20.3%	2i7h	Crystal structure of the nitroreductase-like family protein from bacillus cereus
3	9.0	10	1.35	27.4%	2b67	Crystal structure of the nitroreductase family protein from streptococcus pneumoniae tigr4
4	7.8	10	1.77	27.4%	1ywq	Crystal structure of a nitroreducta   se family protein from bacillus cereus atcc 14579
5	7.5	8	1.79	26.6%	3bm1	Crystal structure of a minimal nitroreductase ydja from escherichia coli k12 with and without fmn cofactor
6	8.7	9	1.86	25.7%	3ek3	Crystal structure of nitroreductase with bound fmn (yp_211706.1) from bacteroides fragilis nctc 9343 at 1.70 a resolution
7	8.1	9	1.57	25.9%	2fre	The crystal structure of the oxidoreductase containing fmn
8	8.1	9	1.80	21.3%	3bem	Crystal structure of putative nitroreductase ydfn (2632848) from bacillus subtilis at 1.65 a resolution
9	7.9	9	1.33	34.3%	3e10	Crystal structure of putative nadh oxidase (np_348178.1) from clostridium acetobutylicum at 1.40 a resolution
10	9.4	11	1.49	25.4%	1bkj	Nadph:fmn oxidoreductase from vibrio harveyi

Shown below is a representation of the 3gfa residues defining the putative active site. The structure indicates that a chloride ion is adjacent to the FMN cofactor.  The structure also shows a methyl-pentane diol from the crystallization solutions bound nearby.

Ligand Summary