ATP binding domain 4 Structures: Difference between revisions
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Note that there is a artificial ligand, TRS (purple) bound to the protein]] | Note that there is a artificial ligand, TRS (purple) bound to the protein]] | ||
[[Image:1RU8 as 2 domain.png|right|thumb|500px|'''Figure 1.2'''. 1RU8 indicates its a dimer]] | [[Image:1RU8 as 2 domain.png|right|thumb|500px|'''Figure 1.2'''. 1RU8 indicates its a dimer]] | ||
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== Secondary Structure and Location of PP-loop == | == Secondary Structure and Location of PP-loop == |
Revision as of 07:30, 16 June 2009
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
Secondary Structure and Location of PP-loop
Electrostatic Surface Potential
Structure Similarities
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
ATP binding Domain 4(1RU8) and Arginosuccinate Synthase (2NZ2)
Highlighted in green is the 2NZ2 while in magenta is the 1RU8. Since 1RU8 has 2 domain, domain B/2 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.
ATP binding Domain 4 (1RU8) and Queuosine Biosynthesis (3BL5)
Surface Cleft and Topography
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
Abstract|
Introductions|
Methods|
Structural Analysis|
Functional Analysis|
Evolutionary Analysis|
Discussions|
Conclusion |
References