3cgh

Protein Summary

Gene BT_3984 Bacteroides thetaiotaomicron VPI-5482 encodes the protein NP_812895 that belongs to the SusD/RagA family (PF07980). SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane. STRING genome context analysis suggests a 0.805 scored link with BT_3983, a putative outer membrane protein involved in nutrient binding.

NP_812895 is the first structure from PFAM family of SusD-like proteins PF07980, which is a large family with over 2000 members involved in nutrient binding. After being produced by Bacteroides thetaiotaomicron, a human gut bacterium, BT_3984 is secreted and becomes a part of an outer membrane bound carbohydrate binding complex.

The fold of 3gch consists of two subdomains with some resemblance to two other known folds. The first domain shows a significant structural similarity to SCOP  alpha-alpha-superhelix fold and especially to the TPR-like superfamily, SuSD-like family (Fig 2), with some traces of sequence similarity. The second subdomain shows much weaker similarity to proteins from the SCOP  alpha/alpha toroid fold (Fig 3). In each case, 3gch contains additional elements that are not seen in either of those folds. Dali top hits are with SusD homologs like PDB:3gzs (Z-scr=49), PDB:3fdh (Z-scr=30), PDB:3ihv (Z-scr=20).

The model solved by JCSG, 3cgh, contains a truncation, with the first 22 amino acids not included in the expression construct. Additionally, residues 23-30 are disordered and not included in the model. There is a zinc atom coordinated by residues HIS 284, CYS 289, GLU 321, and HIS 344.

Figure 1. Overall fold of 3cgh, with zinc shown in grey.



Figure 2. Alignment of 3cgh (blue) with 1hz4 (orange) (Dali Z-scr=6.8).


Figure 3. Alignment of 3cgh (blue) with 1hzf (red) (Dali Z-scr=5.3).

Ligand Summary

Zinc is modeled based on an x-ray flourescence scan, anomalous difference maps, and coordination geometry.

References