Difference between revisions of "Arylformamidase Structure"

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== '''Results''' ==
  
  
== '''Results''' ==
 
  
 
== Structure of Arylformamidase ==
 
== Structure of Arylformamidase ==
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''Image from PDB ProteinWorkshop 1.5''
 
''Image from PDB ProteinWorkshop 1.5''
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'''strand- purple'''
 
'''strand- purple'''
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== '''Interaction of human arylformamidase (AFMID) with other proteins''' ==
 
== '''Interaction of human arylformamidase (AFMID) with other proteins''' ==
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5- Experimental/Biochemical data  
 
5- Experimental/Biochemical data  
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== '''Interaction of  Silicibacter Sp. arylformamidase (AFMID) with other proteins''' ==
 
== '''Interaction of  Silicibacter Sp. arylformamidase (AFMID) with other proteins''' ==
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[[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)
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== '''DALI OUTPUT''' ==
 
== '''DALI OUTPUT''' ==
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'''Metagenomic Archea Carboxylesterase (Chain A ONLY)'''
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'''Figure: Metagenomic Archea Carboxylesterase (Chain A ONLY)'''
  
[[Image:ChainA 2c7b.PNG]]    ''From PDB ProteinWorkshop 1.5''
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[[Image:ChainA 2c7b.PNG]]     
  
 
[[Image:Carboxylase.txt ]]
 
[[Image:Carboxylase.txt ]]
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Note: Chain B not shown
 
Note: Chain B not shown
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''From PDB ProteinWorkshop 1.5''
  
  
'''Archaeoglobus fulgidus Carboxylesterase (Chain A ONLY)'''
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'''Figure: Archaeoglobus fulgidus Carboxylesterase (Chain A ONLY)'''
  
[[Image:ChainA 1jji.PNG]]  '' From PDB ProteinWorkshop 1.5''
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[[Image:ChainA 1jji.PNG]]   
  
 
[[Image:Carboxylesterase (archaeon).txt]]
 
[[Image:Carboxylesterase (archaeon).txt]]
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Note: Chains B, C & D not shown
 
Note: Chains B, C & D not shown
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''From PDB ProteinWorkshop 1.5''
  
  
 
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.
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== '''Secondary structure analysis''' ==
 
== '''Secondary structure analysis''' ==
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'''Archeon Carboxylesterase secondary structure'''
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'''Figure: Archeon Carboxylesterase secondary structure'''
  
 
[[Image:PDBsums.png]]  ''From PDBsum''
 
[[Image:PDBsums.png]]  ''From PDBsum''

Revision as of 05:46, 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

Figure: Arylformamidase (All Chains)


Arylformamidase the whole protein.PNG


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. When crystallizing proteins they often form complexes (dimer, tetramers etc) but that doesn't mean that the functional structure is the same. They could be functional monomers. Those chains exist as individual functional units.

Image from PDB ProteinWorkshop 1.5


Figure:Chain A of arylformamidase


ChainA1.PNG


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.

Image from PDB ProteinWorkshop 1.5

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


Figure: Metagenomic Archea Carboxylesterase (Chain A ONLY)

ChainA 2c7b.PNG

File:Carboxylase.txt

PDB link title

Note: Chain B not shown

From PDB ProteinWorkshop 1.5


Figure: Archaeoglobus fulgidus Carboxylesterase (Chain A ONLY)

ChainA 1jji.PNG

File:Carboxylesterase (archaeon).txt

PDB link title

Note: Chains B, C & D not shown

From PDB ProteinWorkshop 1.5


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]


Figure: 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



Figure: The catalytic triad


Untitled2.PNG


The above image shows the conserved residues of the catalytic triad in arylformamidase, with the unknown ligand (Blue) protruding from a surface groove. The residues are serine 136, Histidine 241 and Glutamate 214. Note: The actual residue numbers are n+1

Image generated using Pymol


Figure: The conserved residues of arylformamidase


Cat triad red.PNG


The blue region shows the residues conserved among species. It is mostly around the unknown ligand. The conserved residues were obtained from observing the clustal alignment.

Image generated using Pymol


Figure: The catalytic triad


CATALYTIC TRIAD 1.PNG

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

From PDB ProteinWorkshop 1.5


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


Cattriad 2c7b.PNG


Figure: The conserved catalytic triad in Metagenomic Archea Carboxylesterase (PDB ID 1JJI)



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