Result of SNAPG

SNAPG Structure

Structure architecture

In order to analyze protein structure of SNAPG, structural comparison to known protein structure is required. An insight to SNAPG structural arrangement provides various informative data on possible protein functions and interactions with another protein and/or DNA. Based on protein families database, Pfam at Sanger, it was found that SNAPG protein matched to Pfam-B protein families and consist of 2 domains, Pfam-B_7270 (PB007270) and Pfam-B_15198 (PB015189) respectively as shown in Figure 3. Both of 2 domains appears to be associated with NSF attachment protein activity [1]. The sequence was also used against InterproScan generated by Profunc that gave an TFR (Tetratricopeptide-like helical) domain classification while that of protein family agrees with Pfam classification. (interproscan)

Figure 1. Ligands interaction to SNAPG chain A. A) Ligands position in the structure are highlighted; B) Secondary structure of SNAPG chain A with ligands interaction indicated; and C) Various ligand interactions with SNAPG by covalent bonds (shown in red color), hydrogen bonding (cyan) and van der waals (green)

Figure 2. Various interaction of sulfanate ions

Figure 3. Two domains of SNAPG protein (chain A)

Structural comparison

Dali webserver is one of the powerful tool to screen any protein that are structurally homologous with our query. Two structurally related proteins with highest Z-value generated by Dali server were chosen for SNAPG structure comparison analysis. These proteins were vesicular transport ptotein sec17 (1qqe) and type 4 fimbrial biogenesis protein (2f17) (refer to Table 1).alto

Table 1. Structure comparison based on Dali results

PDB-chain	Structure	RMSD	Z-value	% identity	Protein
2IFU-A		0.0	37.8	100	Endocytosis/exocytosis. Gamma-SNAP (Danio rerio)
1QQE-A		3.4	23.3	23	Protein binding. Vesicular transport protein sec17(yeast)
2FI7-A		11.6	12.9	14	Protein transport. Type 4 fimbrial biogenesis protein pili (Pseudomonas aeruginosa)

2ifuA, 1qqeA and 2fi7 alignment

Figure 4. Superimposed structures of 2ifuA with 1qqeA (A) and 2ifuA with 2fi7A (B) generated by PyMOL. The 2ifuA is shown in green, 1qq3A in blue and 2fi7A in purple color.

Figure 5. Stucture and sequence alignment of 2ifuA, 1qqeA and 2fi7A generated by STRAP.

physical properties

Figure 6. Hydrophobic and hydrophilic residues of 2ifuA (A) and 1qqeA (B) in front and back view. Amino acid residues with hydrophobic properties such as Ala, Gly, Val, Ile, Phe, and Met were selected and colored in green while that with hydrophilic properties (= Arg, Lys, His, Glu, Asp, Asn, Gln, Thr, Ser, and Cys) were colored in orange

Figure 7. Charged residues of 2ifuA (A) and 1qqeA (B) in front and back view. The sidechains for charged residues indicated as red (negative; Glu and Asp) and blue (positive; Arg, Lys and His).

Figure 8. 2ifuA structures highlighted by chain color ramp (A), hydrophobicity (B) and conformation type (C). Legends are shown.

Figure 9. 2ifuA electrostatic potential map visualised by molecular surface. Computation method that were used are coulumb method.(red= -1.800; white= 0.000; blue= +1.800)

Figure 10.

SNAPG Function

Gene Ontology Annotation by Similarity

AmiGo has been used to find three structured controlled vocabularies that describe gene products of SNAPG in terms of their associated biological processes, cellular components and molecular functions. This protein function is not yet established therefore it is only by similarity (see the figure below).

Figure 11. Gene Ontology: Biological Process, Molecular Function and Cellular Component of SNAP gamma by similarity

Function in the context of Structure

Fold Matching Analysis by ProFunc

SSM (Krissinel and Henrick, 2004) represents several protein that have similar structure to SNAPG associated with function prediction. The most closely related structure is 1qqeA shows 24% fold identity to 2ifuA. This results could be different from DALI results (refers to Table1).

Figure 12. Fold match results for ay64 (chain A)

Conserved Residue Domain

Figure 13. Sequences showing conserved residue between 2ifu, 1qqe and 2FI7 on chain A

Cellular Context

Figure 14. Cellular localisation of human SNAPG on various tissue. Expression of SNAPG is highest in B lymphocytes and bone marrow

Figure 14. Cellular localisation of mouse SNAPG on various tissue. The highest expression of SNAPG is more distributed

SNAPG Evolution

Background

Figure 12. Cladogram treeview of SNAP-gamma Protein

This is the cladogram treeview of SNAP-gamma protein. However, this view is not suitable enough to represent the evolutionary gap between species but this is clearly shows the species name.

Final Tree Analysis

Figure 13. Evolutionary analysis of the tree with radial view (for professional viewer)

Legends:

• Red-dotted sign means boostrap value more than 75.00 or 75%
• any number (in red) located near branching tree indicated boostrap value of the branching tree
• Green Line: The species belongs to Plants group
• Brown Line: Amoeba group
• Purple Line: Parasite type
• Pink Line : The species belongs to Insects Group
• Light Green Line: Worms Group
• Dark Blue Line: Invertebrate
• Red Line: Vertebrate

Other version: Evolutionary analysis of the tree with radial view (for non-professional or common viewer)

Other Attributes

command BLAST

List IDs use as an batch entrez input

List of various alignments of protein

Boostrap value