ATP binding domain 4 Structures

From MDWiki
Revision as of 18:05, 2 June 2009 by Anharmustafa (talk | contribs)
Jump to navigationJump to search

General Properties

General information from PDB indicates that:

(a) 1RU8 is a putative n-type ATP pyrophosphatase isolated from Pyrococcus furiosus, expressed in Escherichia Coli.

(b) Is a member of clan PP-loop

(c) Resolution of 2.7 angstroms, with an r-value of 0.218.

(d) Ligand chemical component identified as TRS (2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL).


Information from SCOP when searched for 1RU8:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
     Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: Adenine nucleotide alpha hydrolase-like [52373]
     core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
  4. Superfamily: Adenine nucleotide alpha hydrolases-like [52402]
     share similar mode of ligand (Adenosine group) binding
     can be subdivided into two group with closer relationships within each group than between the groups; the first three families 
     form one group whereas the last two families form the other group
  5. Family: N-type ATP pyrophosphatases [52403]
  6. Protein: Putative N-type ATP pyrophosphatase PF0828 [102264]
  7. Species: Archaeon Pyrococcus furiosus [TaxId: 2261] [102265]

Surface Structure

Pymol Visualization

Figure 1.0. The three-dimensional structure of secondary structure 1RU8, as generated by PyMOL

Purple- Helix
Yellow - Sheet
Green- Loop


Figure 1.1. The three-dimensional surface structure of 1RU8, as generated by PyMOL. Note that there is a artificial ligand, TRS (purple) bound to the protein
Figure 1.2. 1RU8 indicates its a dimer





















































Secondary Structure and Location of PP-loop

Figure 2.0. Conserved residues of 1RU8 via PDBsum
Figure 2.1. Conserved residues of 1RU8 based on figure 4 visualized in Pymol. Highlighted red is the really conserved region and highlighted blue is the residues that is conserved and interact with the ligand



































Electrostatic Surface Potential

Figure 3. The electrostatic surface potential. Blue colour indicated positive charge and red colour indicated negative charge surface whereas white colour indicated neutral charge

Structure Similarities

Figure 4. The list of structural similarities to 1RU8 obtained using DALI. Highlighted by the box is the most similar structure that has known function which are used in this investigation.

Z score , the statistical significance of the similarity between protein-of-interest and other neighbourhood proteins. The program optimizes a weighted sum of similarities of intramolecular distances.

Root Mean Square Distance (RMSD), root-mean-square deviation of C-alpha atoms in the least-squares superimposition of the structurally equivalent C-alpha atoms. RMSD is not optimized and is only reported for information.

lali, the number of structurally equivalent residues.

nres, or the total number of amino acids in the hit protein.

%id, percentage of identical amino acids over structurally equivalent residues.

Structure Alignment

1RU8 and 2NZ2

Figure 5.0. Structure alignment between 1RU8 and 2NZ2 generated via PyMol-Front view
Figure 5.1. Structure alignment between 1RU8 and 2NZ2 generated via PyMol-Back view





















Highlighted in green is the 2NZ2 while in magenta is the 1RU8. Since 1RU8 has 2 domain, domain B is coloured darker in magenta for differentiation. There are 2 ligand indicated by the yellow (Citrulline) and red (ATP) spheres from 2NZ2. Highlighted also is the conserved region of PP-loop in pink and blue for 1RU8 and 2NZ2 respectively.

1RU8 and 3BL5

Figure 6. Structure alignment between 1RU8 and 3BL5 generated via PyMol













Surface Cleft and Topography

Figure 7.0. The topology of 1RU8 generated via CASTp
Figure 7.1. The topology of 2NZ2 generated via CASTp
Figure 7.2. The topology of 3BL5 generated via CASTp

























The volume and size of the cleft of between protein indicated similarity between 1RU8 and 2NZ2. While 3BL5 has less similarity when compared to both 1RU8 and 2NZ2













>



Discussion

IRU8 is a protein with an unknown function. The crystallization of 1RU8 was done from Pyrococcus furiosus that is expressed in Escherichia Coli with resolution of 2.7 angstroms and an r-value of 0.218. Since the function of this protein is still unsure, artificial chemical ligand, TRS(2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL)was used in the crystallization. Moreover, the actual ligand still cannot be found even after we have looked into research papers. Hence, deduction of the ligand of this protein can only be done, based on the protein that has similar function or structure.

From the struture obtained from the PyMOL, visualization of the secondary structure, its surface properties covering positively charged regions and negatively charged regions, its domains as well as ligand binding sites and surface clefts, and also conservation of residues across different species can be done. It was observed that detailed secondary structure can be determined using PDBsum where conserved residues, protein motif and possible ligand binding site was highlighted (Figure 2). Information from the PDB and SCOP has indicated that 1RU8 is a clan of PP-loop which is the strongly conserved motif SGGKD at the N terminus. This PP-loop was significant as it is the most conserved and is likely to give function to our protein. Besides that, From CATH domain database, two main domains were found in 1RU8. The first domain ranges from residue 3-97 and while the second domain residues from 98-232. Topology of Domain 1 is known to be of Rossmann A-B-A fold, and the superfamily of PP-loop is presence in this domain. Domain 2 is A-B complex classified in CATH.

Structural alignment via DALI enabled us to obtained proteins that is similar in terms of structure relatedness to 1RU8. Based on the DALI output, 2d13 is rejected since it is a hypothetical protein ph1257 that has no known function to compare to. Thus, 2nz2 and 3b15 was chosen since it is the most similar based on the z-score. Information on 2nz2 and 3bl5 by InterPro indicated that both has PP-loop. Hence, emphasizing again the importance of PP-loop to 1RU8's function. These 2 protein was crucial since analysis based on the structural alignment and cleft size and volume was done and has been a valuable indicator of 1RU8's function.

Structural alignment of 1RU8 with 2NZ2 and with 3BL5 (Figure 5 and 6) show that 1RU8 and 2NZ2 has the most similar alignment. Since 2NZ2 has a known function which is to catalyzes the transformation of citrulline and aspartate into argininosuccinate and pyrophosphate using the hydrolysis of ATP to AMP and pyrophosphate. Hence, it is inferred that since the active site or the binding site structure is quite similar(based on the structural alignment), the substrate for 1RU8 must then have similar properties and organization of 2nz2 substrate (ATP and Citrulline) in a certain extent. Based on Figure 5, ATP is located near the PP-loop and Citrulline quite far from the loop which is supporting the fact that ATP is hydolysed for citrulline to activate. Hence, similar mechanism may be imply to 1RU8.

Pockets and cavities in the structure is often associated with binding sites and active sites of proteins. Identification and measurements of surface accessible pockets as well as interior inaccessible cavities of 1RU8, 2NZ2 and 3BL5 were obtained from CASTp (Figure 7.0 to 7.2).Laskowski R.A inferred that cleft volumes in proteins relate to their molecular interactions and functions. It was observed from the result, cleft of 1RU8 is quite similar in size and volume to 2NZ2 which suggesting that 1RU8 ligand may have similar size to 2NZ2 ligand. Thus, supporting the hypothesis that 1RU8 substrate or ligand may have similar properties to 2NZ2 substrate.