Result of SNAPG

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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. SNAP-gamma

Figure 2. 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. Sulfanate ions interact mainly hy hydrogen bonding while MSE by covalent bonds (shown in red color), hydrogen bonding (cyan) and van der waals (green).

Figure 3. Various interaction of sulfanate ions to different residues of SNAPG

Figure 4. Two domains of SNAPG protein (chain A) obtained from Pfam at Sanger. Residue 7-66 aligned with Pfam-B_7270 domain and that of 87-307 with Pfam-B_15198.

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).

Table 1. Structure comparison based on Dali results
PDB-chain Structure RMSD Z-value % identity Protein
0.0 37.8 100 Endocytosis/exocytosis. Gamma-SNAP (Danio rerio)
1qqe asym r 250.jpg
3.4 23.3 23 Protein binding. Vesicular transport protein sec17(yeast)
2fi7 asym r 250.jpg
11.6 12.9 14 Protein transport. Type 4 fimbrial biogenesis protein pili (Pseudomonas aeruginosa)

2ifuA, 1qqeA and 2fi7 alignment

physical properties

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 SNAP-gamma 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. Secondary structures are highlighted with red

Sequence Motif

Aromatic-di-Alanine (AdAR) repeat was found in NSF attachment proteins (SNAP-gamma). Its structure is similar to that found in TPR-1 (belongs to Tetratrico peptide repeat family). Get the link

Figure 14. TPR family motif was linked to SNAP-gamma

Genomic Context

Figure 15. SNAP gamma is conserved on several organisms genome

Cellular Context

Figure 16. Cellular localisation of human SNAPG on various tissue. Expression of SNAPG is highest in B lymphocytes and bone marrow
Figure 17. Cellular localisation of mouse SNAPG on various tissue. The highest expression of SNAPG is more distributed

SNAPG Evolution


Figure 18. 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 19. Evolutionary analysis of the tree with radial view (for professional viewer)


  • 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

Back to Scientific Report of N-ethylmaleide-sensitive factor attachment protein, gamma