Chromosome 1 open reading frame 41 Structure: Difference between revisions

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'''Protein Structure'''
'''1)Structural similarities'''


PDB ID: 1TVG
[[Image:Picture 1.png|centre|framed|'''Figure 5:''' DALI result showing the first 35 proteins that have similar structures to c1orf41. Even though the proteins are similar in structure they have very little sequence identity to c1orf41. 1xpw is c1orf41 but the structure was solved by NMR.]]
Information from the PDB stated that x-ray diffraction was sued to solve the structure of this protein with an R value of 0.215 and at 1.6Å. Two ligands were present in the crystal structure, a calcium (II) ion and a samarium (III) ion. This protein has 153 residues and its secondary structure consists of two helices and nine beta sheet strands.  


Scop result
Root: scop
Class: All beta proteins [48724]
Fold: Galactose-binding domain-like [49784]
sandwich; 9 strands in 2 sheets; jelly-roll
Superfamily: Galactose-binding domain-like [49785]
uperfamily
Family: APC10-like [69210]
Pfam 03256
Protein: Placental protein 25, pp25 [117104]
Species: Human (Homo sapiens) [TaxId: 9606] [117105]
SQ Q9Y547


'''2)Domain Classification'''


  [[Image:PDB sum 2.PNG]]
[[Image:1TVG pfam.png|centre|framed|'''Figure 6:''' Pfam result indicated that our protein has a F5/8 type C domain, also known as the discoidin domain which is apart of galactose binding domain super family.]]
 
Figure 1: Above is the representation of c1orf41 secondary structure as presented in PDBsum.




Tertiary structure
'''3)Protein Structure'''


  [[Image:Pymol ss1.PNG]]
Secondary structure


Figure 2: This  cartoon representation of c1orf41 shows that this protein is monomeric, consisting of a single domain. the fold of the protein is a jelly roll barrel where four pairs of anti-parallel beta strands are organised to form a barrel-like structure.  
[[Image:PDB sum 2.PNG|centre|framed|'''Figure 1:''' Representation of c1orf41 secondary structure as presented in PDBsum.]]


----
'''Structure analysis'''


'''1)Structure similarities'''
Tertiary structure


DALI was used to find protein that are similar in structure to 1TVG. The results showed that sialidases, alpha-N-acetylglucosaminidases and galactose oxidases have similar structure to our protein as presented below.
[[Image:1tvg ani.gif|centre|framed|'''Figure 2:''' This protein is monomeric, consisting of a single domain. There are 8 beta strands (yellow) and 2 alpha helices (purple). The secondary structures are folded into jelly roll barrel where four pairs of anti-parallel beta strands are organised to form a barrel-like structure.]]


[[Image:Picture 1.png]]
'''2)Domain Classification'''


Pfam result indicated that our protein has a F5/8 type C domain, also known as the discoidin domain which is apart of galactose binding domain super family.  
[[Image:Charge surface ani.gif|centre|framed|'''Figure 3:''' Electrostatic charge distribution on the surface of c1orf41.]]


[[Image:1TVG pfam.png]]


Closer inspection of the other proteins from the DALI result showed that they also have discoidin domain in their structures.
[[Image:1tvg surface.png|centre|framed|'''Figure 4:''' Surface representation of c1orf41. The Ca (II) ion is located within a pocket of the protein. Sm (III) interacts with Asp92 on the protein but its presence was probably due to the method used in solving the phase problem during structure solution using x-ray crystallogrophy.]]




'''3)Possible ligand binding sites'''


Observations and comparisons of several proteins from the DALI result with our protein, there is a similar position on each proteins where a metal ion is located.
'''4)Possible ligand binding sites'''




[[Image:1tvg ligand1.png]]
[[Image:1tvg ligand1.png|centre|framed|'''Figure 7:''' This figure shows the position where calcium (II) ion (yellow) is located in within a loop of c1orf41 structure. This loop where metal ion is coordinated to was also observed in several proteins from the DALI result.]]


This figure shows the position where calcium (II) ion (yellow) is located in within our protein structure. This loop structure was also observed in several top proteins in the DALI result.


[[Image:1gog Na.png]]
[[Image:1gog Na.png|centre|framed|]]  


Shown is the discoidin domain of galactose oxidase and a sodium ion (purple).
[[Image:2bzd discoidin2.png|centre|framed|'''Figure 8:'''Shown at the top is the discoidin domain of galactose oxidase with a sodium ion (purple) located within a loop. The bottom figure is bacterial sialidase discoidin domain with a sodium ion (purple) and a beta-D-galactose molecule. The sodium ion is also located i within a loop.]]




[[Image:2bzd discoidin2.png]]
[[Image:1tvg castp3.PNG|centre|framed|'''Figure 9:'''CastP identified a surface cleft that is located at the loop position.]]


Shown is the discoidin domain of bacterial sialidase and a sodium ion (purple) and a beta-D-galactose molecule.


CastP also showed a surface cleft that is includes the loop region as shown below.
[[Image:1tvg ca res2.PNG|centre|framed|'''Figure 10:'''Pymol figure displaying possible metal binding position on c1orf41. Pink are the residues that may be involved in coordinating the metal and yellow is the calcium ion. The residues are based on CastP result. The aspartate and glutamate residues are likely to be important in binding positively charged metal ion]]


[[Image:1tvg castp2.png]]




Below is a possible metal binding position on c1orf41. Orange is the residues that may be involved in coordinating the metal and blue is the calcium ion.
[[Image:Profunc nest.PNG|centre|framed|'''Figure 11:'''Nest 1 and 2 had scores higher than 2. So, they are more likely to be functional. His54 and Lys55 NH atoms are accessible from a large surface cleft of the protein. The cleft is also deep indicating that the nest is functionally important. The residues of Nest 2 are part of the loop that coordinates the Ca (II)ion.]]


[[Image:1tvg residue metal.png]]
[[Image:1tvg nests2.png|centre|framed|'''Figure 12:'''Pymol representation of Nest 1 and 2.]]




Nest analysis by Profunc suggested two other ligand binding sites.
[[Image:Surface nest3.PNG|centre|framed|'''Figure 13:'''Arrows indicating the pockets of the nests that may be accessible to ligands.]]


[[Image:Nest analysis result.PNG]]


The locations of the binding sites are shown below. CastP also predicted surface clefts similar to the erea of the nests.


[[Image:1tvg nests.png]]
[[Chromosome 1 open reading frame 41 Evolution|Next]]

Latest revision as of 06:25, 16 June 2009

1)Structural similarities


Figure 5: DALI result showing the first 35 proteins that have similar structures to c1orf41. Even though the proteins are similar in structure they have very little sequence identity to c1orf41. 1xpw is c1orf41 but the structure was solved by NMR.


2)Domain Classification

Figure 6: Pfam result indicated that our protein has a F5/8 type C domain, also known as the discoidin domain which is apart of galactose binding domain super family.


3)Protein Structure

Secondary structure

Figure 1: Representation of c1orf41 secondary structure as presented in PDBsum.


Tertiary structure

Figure 2: This protein is monomeric, consisting of a single domain. There are 8 beta strands (yellow) and 2 alpha helices (purple). The secondary structures are folded into jelly roll barrel where four pairs of anti-parallel beta strands are organised to form a barrel-like structure.


Figure 3: Electrostatic charge distribution on the surface of c1orf41.


Figure 4: Surface representation of c1orf41. The Ca (II) ion is located within a pocket of the protein. Sm (III) interacts with Asp92 on the protein but its presence was probably due to the method used in solving the phase problem during structure solution using x-ray crystallogrophy.


4)Possible ligand binding sites


Figure 7: This figure shows the position where calcium (II) ion (yellow) is located in within a loop of c1orf41 structure. This loop where metal ion is coordinated to was also observed in several proteins from the DALI result.


1gog Na.png
Figure 8:Shown at the top is the discoidin domain of galactose oxidase with a sodium ion (purple) located within a loop. The bottom figure is bacterial sialidase discoidin domain with a sodium ion (purple) and a beta-D-galactose molecule. The sodium ion is also located i within a loop.


Figure 9:CastP identified a surface cleft that is located at the loop position.


Figure 10:Pymol figure displaying possible metal binding position on c1orf41. Pink are the residues that may be involved in coordinating the metal and yellow is the calcium ion. The residues are based on CastP result. The aspartate and glutamate residues are likely to be important in binding positively charged metal ion


Figure 11:Nest 1 and 2 had scores higher than 2. So, they are more likely to be functional. His54 and Lys55 NH atoms are accessible from a large surface cleft of the protein. The cleft is also deep indicating that the nest is functionally important. The residues of Nest 2 are part of the loop that coordinates the Ca (II)ion.


Figure 12:Pymol representation of Nest 1 and 2.


Figure 13:Arrows indicating the pockets of the nests that may be accessible to ligands.


Next

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