3due

Protein Summary

A manuscript describing this structure has been published in 2010:

"The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.", Das, D. et. al. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1265-73.

Gene BVU2987 from Bacteroides vulgatus ATCC 8482 ecodes the YP_001300247 sequence, a putative periplasmic protein belonging to the DUF2874 group (PF11396). This bacterium is one of the most predominant microorganisms in the human gut. Based on the presence of a signalling sequence predicted by  TMHMM and SignalP with the  cleavage site between residues 20-21 it is believed to be secreted. The solved structure is the construct from amino acids 20-145 and has the signal sequence removed.

Its a first structural representative of a large protein family (>100 members) present mostly in different species of Bacteroides and Campylobacters, , but also in Porphyromonas gingivalis (main agent of periodontal disease) and human oral and gut microbiome. Proteins in this family are annotated as putative periplasmic proteins and conserved hypothetical proteins, but none of them have been studied experimentally. FFAS detects similarity betweeen this family and an N-terminal domain from the  COG3212: Predicted membrane protein (FFAS score: -15.700. This is a much larger family (>400 memebers) with a (predicted) peptidase domain at the C-terminal.

Pre-SCOP classifies 3due in the alpha+beta class, BLIP-like fold, BT0923-like (super)family. 3due is present as a monomer in the asymmetric unit of the unit cell of the crystal structure. Crystal packing analysis suggests that the favored oligomeric form in solution should be a monomer.

A Dali search with 3due as query, provides hits with 3db7 (Z=24) and 3elg (Z=20). A weak hit is with 2g2u (Z=5).

SSM results have very low scores. The top 2 hits have score with Q-value=0.19 and are with beta-lactamase inhibitory protein (BLIP), PDB ids 2b5r and 2g2w.

FATCAT produces some significant hits to BLIP (PDB code: 2g2u (exp=0.00105, same paper as 2g2w) and 2ogq (exp=0.00285)) by flexible alignment, as well as to a recently solved JCSG structure 3d4e (2.7A RMSD over 100 aa with 6% sequence ID).

Superposition of this protein with that of the 2g2u (green, Ref1, ~2.6A rmsd) shows their structural similarity (with a sequence identity of ~5%). The loops between the beta-strands in this protein are shorter than in the BLIP. The start of the N-terminal helix in the two proteins is also different. The amino acids from BLIP that are implicated in the interaction with beta-lactamase (W150, E31, D49, R160, Y115, W162, F142, K74 and Y143) are not conserved in this protein.

Superimposition with a portion of 2ogq (orange, Ref2, ~3.2A rmsd): This is the C-terminal regulatory domain (PB domain) of the Plk1 Polo-like kinase. The characteristic PB sequence of Plk1 is not conserved in this protein. The sequence identity between these two proteins is ~5%.

Cacodylate from the crystallization condtion has been modeled in the structure.

References:

1. Reynolds, K.A.,  Thomson, J.M.,  Corbett, K.D.,  Bethel, C.R.,  Berger, J.M.,  Kirsch, J.F.,  Bonomo, R.A.,  Handel, T.M. (2006) Structural and Computational Characterization of the SHV-1 beta-Lactamase-beta-Lactamase Inhibitor Protein Interface. J.Biol.Chem. 281: 26745-26753

2. Garcia-Alvarez, B.,  de Carcer, G.,  Ibanez, S.,  Bragado-Nilsson, E.,  Montoya, G. (2007) Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization. Proc.Natl.Acad.Sci.Usa 104: 3107-3112

Ligand Summary