Difference between revisions of "Arylformamidase Structure"

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=='''Methods'''==
 
=='''Methods'''==
 
 
  
 
The structure of arylfromamidase was obtained from RCSB Protein Data Bank (PDB ID: 2PBL).
 
The structure of arylfromamidase was obtained from RCSB Protein Data Bank (PDB ID: 2PBL).
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== '''Results''' ==
 
== '''Results''' ==
 +
 
== Structure of Arylformamidase ==
 
== Structure of Arylformamidase ==
 
  
  
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----
 
 
[[Image:Arylformamidase the whole protein.PNG]]        ''From PDB ProteinWorkshop 1.5''
 
[[Image:Arylformamidase the whole protein.PNG]]        ''From PDB ProteinWorkshop 1.5''
 
  
  
 
''The image above shows the chains A (upper right), B (upper left), C (lower right) & D (lower left) interacting. The molecules in the middle of chains A & B and chains C & D  is phosphate ion (PO4). The green molecule between chain B & D is a magnesium ion (Mg). These ions aren't biologically significant and could only be an artefact. Those chains exist as indivitual functional units.''
 
''The image above shows the chains A (upper right), B (upper left), C (lower right) & D (lower left) interacting. The molecules in the middle of chains A & B and chains C & D  is phosphate ion (PO4). The green molecule between chain B & D is a magnesium ion (Mg). These ions aren't biologically significant and could only be an artefact. Those chains exist as indivitual functional units.''
 
 
 
  
  
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''The red molecule in the middle is an unknown ligand containing a ring composed of 9 oxygen molecules. The green sphere is a chloride ion.''
 
''The red molecule in the middle is an unknown ligand containing a ring composed of 9 oxygen molecules. The green sphere is a chloride ion.''
 +
  
 
'''''The protein backbone is coloured by conformation type:'''''
 
'''''The protein backbone is coloured by conformation type:'''''
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'''strand- purple'''
 
'''strand- purple'''
  
== '''2. Interaction of human arylformamidase (AFMID) with other proteins''' ==
+
 
 +
 
 +
== '''Interaction of human arylformamidase (AFMID) with other proteins''' ==
  
  
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+
== '''Interaction of  Silicibacter Sp. arylformamidase (AFMID) with other proteins''' ==
== '''3. Interaction of  Silicibacter Sp. arylformamidase (AFMID) with other proteins''' ==
 
  
 
[[Image:Examplec.jpg]]
 
[[Image:Examplec.jpg]]
 
  
  
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 +
There is no significant evidence for these interactions (score= ~0.5)
  
There is no significant evidence for these interactions (score= ~0.5)
 
  
 +
== '''DALI OUTPUT''' ==
  
== '''4. DALI OUTPUT''' ==
 
  
 
The DALI tool produces proteins that are structurally similar to the protein of interest.  
 
The DALI tool produces proteins that are structurally similar to the protein of interest.  
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[[Image:DALI RESULT.txt]]
 
[[Image:DALI RESULT.txt]]
 
 
  
  
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Both of the above Archaeal carboxylesterases' chains exist as monomers (from literature). Hence it is expected that our protein exists as a monomer but during crystalization it interacts with its chains.
 
Both of the above Archaeal carboxylesterases' chains exist as monomers (from literature). Hence it is expected that our protein exists as a monomer but during crystalization it interacts with its chains.
  
== '''5. Secondary structure analysis''' ==
+
== '''Secondary structure analysis''' ==
 
 
  
  
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== '''6. The conservation of the ser/his/asp catalytic triad''' ==
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== '''The conservation of the ser/his/asp catalytic triad''' ==
  
 
[[Image:Catalytic triad conversation.PNG]]
 
[[Image:Catalytic triad conversation.PNG]]
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''Blue indicates semi-conservation''
 
''Blue indicates semi-conservation''
 
 
  
  

Revision as of 02:54, 3 June 2008

Methods

The structure of arylfromamidase was obtained from RCSB Protein Data Bank (PDB ID: 2PBL). http://www.rcsb.org/pdb/home/home.do

The predicted interaction arylformamidase with other proteins was determined using the STRING database (STRING: Search Tool for the Retrieval of Interacting Genes/Proteins). http://string.embl.de//

The DALI database was used for the structural comparison of arylformamidase with other proteins. http://ekhidna.biocenter.helsinki.fi/dali_server/

PDBsum database was used to determine the secondary structure of arylformamidase. http://www.ebi.ac.uk/pdbsum/



Results

Structure of Arylformamidase

Arylformamidase (All Chains)


Arylformamidase the whole protein.PNG From PDB ProteinWorkshop 1.5


The image above shows the chains A (upper right), B (upper left), C (lower right) & D (lower left) interacting. The molecules in the middle of chains A & B and chains C & D is phosphate ion (PO4). The green molecule between chain B & D is a magnesium ion (Mg). These ions aren't biologically significant and could only be an artefact. Those chains exist as indivitual functional units.


Chain A of arylformamidase


ChainA1.PNG From PDB ProteinWorkshop 1.5


The red molecule in the middle is an unknown ligand containing a ring composed of 9 oxygen molecules. The green sphere is a chloride ion.


The protein backbone is coloured by conformation type:

Turn - blue

Coil- pink

Helix- green

strand- purple


Interaction of human arylformamidase (AFMID) with other proteins

Confidence interaction with names.png


The interaction between the proteins have been determined from curated STRING database (significant score). However there is no significant evidence for:

1- Neighborhood in the genome

2- Gene fusions

3- Cooccurence across genomes

4- Co-Expression

5- Experimental/Biochemical data


Interaction of Silicibacter Sp. arylformamidase (AFMID) with other proteins

Examplec.jpg


TM1040_2226 Tryptophan 2,3-dioxygenase (279 aa)

TM1040_2225 Kynureninase (396 aa)

TM1040_2493 Succinic semialdehyde dehydrogenase (490 aa)

TM1040_1862 Hypothetical protein (212 aa)

TM1040_2491 Creatinase (402 aa)

TM1040_2736 Transketolase, putative (794 aa)


There is no significant evidence for these interactions (score= ~0.5)


DALI OUTPUT

The DALI tool produces proteins that are structurally similar to the protein of interest.

The search result showed similarities to mostly carboxylesterases/hydrolases. Hence there is strong evidence that our protein might also be a carboxylesterase.

File:DALI RESULT.txt


Metagenomic Archea Carboxylesterase (Chain A ONLY)

ChainA 2c7b.PNG From PDB ProteinWorkshop 1.5

File:Carboxylase.txt

PDB link title

Note: Chain B not shown


Archaeoglobus fulgidus Carboxylesterase (Chain A ONLY)

ChainA 1jji.PNG From PDB ProteinWorkshop 1.5

File:Carboxylesterase (archaeon).txt

PDB link title

Note: Chains B, C & D not shown


Both of the above Archaeal carboxylesterases' chains exist as monomers (from literature). Hence it is expected that our protein exists as a monomer but during crystalization it interacts with its chains.

Secondary structure analysis

PDBSum output for arylformamidase

PDBSum pblA.PNG

PDBSUM [1]


Archeon Carboxylesterase secondary structure

PDBsums.png From PDBsum


The conservation of the ser/his/asp catalytic triad

Catalytic triad conversation.PNG

Yellow indicates conservation

Blue indicates semi-conservation


Untitled2.PNG Image generated using Pymol


The above image shows the conserved residues of catalytic triad in arylformamidase, with the unknown ligand (Blue) protruding from a surface groove.

SER 136

HIS 241

GLU 214



The below image shows the distance between the catalytic triad conserved residues and how each amino acid is linked to a turn region.

CATALYTIC TRIAD 1.PNG From PDB ProteinWorkshop 1.5


The conserved catalytic triad in Metagenomic Archea Carboxylesterase (PDB ID 2C7B)

Cattriad 2c7b.PNG

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