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Results: 9

1.
Figure 7

Figure 7. Basic Trimer Unit.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

Basic trimeric unit of the hypothetical protein (VCO395_1035) was formed by superimposing the monomer into the trimeric unit of template (PDB ID: 3STJ chain A, B & C).

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
2.
Figure 5

Figure 5. Predicted catalytic triad of model VCO395_1035.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

The cartoon and surface representation of model VCO395_1035 showing predicted catalytic triad residue Ser12-His50-Leu52 along with along with substrate (cyan) bound to active site in Oxyanion hole (ox).

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
3.
Figure 3

Figure 3. Structural alignment of protease domain.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

The cartoon representation of protease domain of model VCO395_1035 (magenta) aligned with template 3STJ (light orange) showing conserved Ser53 with DegQ Ser214 which is one of catalytic triad residue of DegQ along with substrate (cyan) bound to active site in Oxyanion hole(ox).

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
4.
Figure 8

Figure 8. Mechanism of Protease activity.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

Illustration of the activation mechanism: PDZ1→L3→LD/L1/L3. The R37 of loop L3 interact with G200 of PDZ1 domain which allows Q26 of the loop L3 to interact with the residue I16 of loop LD in the adjacent protease shown in * mark. This may induce remodeling of the proteolytic sites and functional catalytic triad set up between S12 of loop LD and H50 & L52 of loop L1.

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
5.
Figure 6

Figure 6. Organization of Active and Inactive form of serine containing proteolytic active site and Catalytic triad.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

A. Substrate binding site of inactive form of protease domain modeled using template 3STI. B. Substrate binding site of active form of protease domain modeled using template 3STJ. C. The orientation and Cα distance between the catalytic triad molecules in the inactive form. D. The orientation and Cα distance between the catalytic triad molecules in the active form.

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
6.
Figure 9

Figure 9. Surface electrostatic potential calculated by PyMOL.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

The positive charge shown in Blue and negative charge shown in Red. A. The active site of protease and PDZ1 domain showing more positively charge and less neutral environment. B. The outer surface of VCO395_1035 showing the blue patches spreads all over the molecule. The positive charge shown in rectangular frame is aggregated from Argine and Lysine residue. The inset shows orientation of Arg-164 & 227 and Lys-226 residue in cartoon representation, which are predicted to interact with outer membrane.

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
7.
Figure 4

Figure 4. Active site and Protein-substrate interaction using Hex 5.0.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

A. The surface view of protease domain containing active site showing the oxyanion hole and properly oriented shallow S1 hydrophobic pocket. B. The surface view of PDZ1 containing hydrophobic binding groove formed by CBL and α7-Helix showing shallow P0 and P−2 substrate binding pocket. C. The C-terminal of poly-alanine peptide substrate (blue) docked into active side of protease domain. D. The C-terminal of poly-alanine peptide substrate (blue) docked into active side of PDZ1 domain via β-aggumentation. E. The superimposition of substrate docked into the protease active site (blue) with respective to template (3STJ) substrate (red). F. The superimposition of substrate docked into the active site PDZ1 domain (blue) with respective to template (3STJ) substrate (red).

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
8.
Figure 2

Figure 2. Characterization of Homology Model of VCO395_1035.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

A. The cartoon representation of 3D modeled structure of VCO395_1035 using PDB ID: 3STJ. Helix (blue), sheets (Purple) and loops (Sky Blue). B. The β-barrel like structure of protease Domain of VCO395_1035 showing active site loops LD: Activation loop, L1: Oxyanion loop, L2: Substrate specificity and L3: Regulatory loop along with interdomain linker (IDL) helix. ML 1: Modeled loop 1 in Protease domain (residue 79–89) on FALC-Loop server indicated as α1-helix. C. The PDZ1 Domain of VCO395_1035, showing flexible carboxylate binding loop (CBL) and interacting clamp (IC). ML 2: Modeled loop 2 in PDZ1 domain (residue 176–189) on FALC-Loop server indicated as α6-helix.

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.
9.
Figure 1

Figure 1. Sequence alignment of VCO395_1035 with E. coli DegQ.. From: In-Silico Structural and Functional Characterization of a V. cholerae O395 Hypothetical Protein Containing a PDZ1 and an Uncommon Protease Domain.

A. Sequence alignment of the query (vib1035) and the E. coli DegQ (EC_DegQ). The ‘*’ indicate the conserved amino acids; ‘:’ represents similar group of amino acids. B. Sequence alignment used for 3D-modeling of VCO395_1035 using E. coli DegQ as template (PDB ID: 3STJ). The blue arrows indicate β sheets, orange bars indicate helix and the yellow bars indicate loops. The deep blue color indicates identical amino acids; lighter blue colors indicate similar and weakly similar amino acids. The two major loop modeled to their corresponding secondary structure were shown in violet color. The predicted catalytic triad residue Ser12-His50-Leu52 indicated by ‘*’ and conserved Ser53 residue with DegQ Ser187 which is one of catalytic triad residue of DegQ of E. coli indicated by down arrow.

Avirup Dutta, et al. PLoS One. 2013;8(2):e56725.

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