Difference between revisions of "Arylformamidase Structure"

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== 1. Structure of Arylformamidase ==
+
=='''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//
  
'''Arylformamidase'''
+
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/
  
----
 
[[Image:Arylformamidase the whole protein.PNG]]        ''From PDB ProteinWorkshop 1.5''
 
  
  
 +
== '''Results''' ==
  
''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.''
 
  
 +
== Structure of Arylformamidase ==
  
 +
Structure was determined using X-ray diffraction by the Joint Center for Structural Genomics (JCSG). The organism is Silicibacter SP. TM1040 and the protein expression system is Escherichia Coli (vector type: plasmid). The resolution is 1.79 A with R-value of 0.224 and R-free value of 0.270. The closer the R values are to each other, the better the quality of the structure.
  
  
'''''Chain A'' of arylformamidase'''
 
  
  
[[Image:ChainA1.PNG]]   ''From PDB ProteinWorkshop 1.5''
+
'''Figure: Arylformamidase (All Chains)'''
 +
 
 +
 
 +
[[Image: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. The chains in the protein of interest exist as individual functional units because in the PDB file it assumes the functional biological molecule as a monomer.''
 +
 
 +
''Image from PDB ProteinWorkshop 1.5''
 +
 
 +
 
 +
 
 +
'''Figure:''Chain A'' of arylformamidase'''
 +
 
 +
 
 +
[[Image: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.''
 
''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:'''''
 
'''''The protein backbone is coloured by conformation type:'''''
  
'''Turn - blue'''
+
'''''Turn - blue'''''
  
'''Coil- pink'''
+
'''''Coil- pink'''''
  
'''Helix- green'''
+
'''''Helix- green'''''
  
'''strand- purple'''
+
'''''strand- purple'''''
  
 +
== '''Interaction of human arylformamidase (AFMID) with other proteins''' ==
  
 
 
== '''2. Interaction of human arylformamidase (AFMID) with other proteins''' ==
 
  
  
Line 43: Line 62:
  
  
The interaction between the proteins have been determined from curated STRING database (significant score). However there is no significant evidence for:
+
''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
+
''1- Neighborhood in the genome''
 
   
 
   
2- Gene fusions    
+
''2- Gene fusions ''   
 
   
 
   
3- Cooccurence across genomes  
+
''3- Cooccurence across genomes ''
 
   
 
   
4- Co-Expression    
+
''4- Co-Expression '' 
 
   
 
   
5- Experimental/Biochemical data  
+
''5- Experimental/Biochemical data''
  
 +
== '''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]]
 
  
  
Line 76: Line 94:
  
  
 +
''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.  
Line 90: Line 108:
  
  
 +
'''Figure: Metagenomic Archea Carboxylesterase (Chain A ONLY)'''
  
 
+
[[Image:ChainA 2c7b.PNG]]     
'''Metagenomic Archea Carboxylesterase A chain'''
 
 
 
[[Image:Carboxylase A chain.PNG]]    ''From PDB ProteinWorkshop 1.5''
 
  
 
[[Image:Carboxylase.txt ]]
 
[[Image:Carboxylase.txt ]]
Line 100: Line 116:
 
'''PDB''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=2C7B link title]
 
'''PDB''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=2C7B link title]
  
 +
''Note: Chain B not shown''
 +
 +
''From PDB ProteinWorkshop 1.5''
  
  
'''Archaeoglobus fulgidus Carboxylesterase (Chains A)'''
+
'''Figure: Archaeoglobus fulgidus Carboxylesterase (Chain A ONLY)'''
  
[[Image:ChainA 1jji.PNG]]  '' From PDB ProteinWorkshop 1.5''
+
[[Image:ChainA 1jji.PNG]]   
  
 
[[Image:Carboxylesterase (archaeon).txt]]
 
[[Image:Carboxylesterase (archaeon).txt]]
Line 110: Line 129:
 
'''PDB''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1JJI link title]
 
'''PDB''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1JJI link title]
  
 +
''Note: Chains B, C & D not shown''
  
 +
''From PDB ProteinWorkshop 1.5''
  
These 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''' ==
+
''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''' ==
  
  
Line 126: Line 147:
  
  
'''Archeon Carboxylesterase secondary structure'''
+
'''Figure: Archeon Carboxylesterase secondary structure'''
  
[[Image:PDBsums.png]]  ''From PDBsum''
+
[[Image:Pdbsums archeal.PNG]]   
  
  
 +
''The secondary structure shows the conservation of the order of different conformation types between the protein of interest and the archaeal carboxylesterases.''
  
 +
''Images from PDBsum''
  
 
+
== '''The conservation of the ser/his/asp catalytic triad''' ==
== '''6. The conservation of the ser/his/asp catalytic triad''' ==
 
  
 
[[Image:Catalytic triad conversation.PNG]]
 
[[Image:Catalytic triad conversation.PNG]]
Line 145: Line 167:
  
  
[[Image:Untitled2.PNG]]      ''Image generated using Pymol''  
+
'''Figure: The catalytic triad'''
  
  
The above image shows the conserved residues of catalytic triad in arylformamidase, with the unknown ligand (Blue) protruding from a surface groove.
+
[[Image:Untitled2.PNG]]
  
SER 136
 
  
HIS 241
+
''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''
  
GLU 214
+
''Image generated using Pymol''
  
  
 +
'''Figure: The conserved residues of arylformamidase'''
  
  
The below image shows the distance between the catalytic triad conserved residues and how each amino acid is linked to a turn region.
+
[[Image:Cat triad red.PNG]]
  
[[Image:CATALYTIC TRIAD 1.PNG]]  '' From PDB ProteinWorkshop 1.5''
 
  
Turn -  blue
+
''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.''
  
Coil-  pink
+
''Image generated using Pymol''
  
Helix-  green
 
  
strand- purple
+
'''Figure: The catalytic triad'''
  
  
 +
[[Image: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. This catalytic triad is also conserved in the Metagenomic Archea Carboxylesterase (PDB ID 2C7B) and the Archaeoglobus fulgidus Carboxylesterase (PDB ID 1JJI)''
 +
 +
'' From PDB ProteinWorkshop 1.5''
 +
 +
 +
 +
'''Figure: The conserved catalytic triad in Archaeoglobus fulgidus Carboxylesterase (PDB ID 1JJI)'''
 +
 +
 +
 +
[[Image:Cat triad 1jji.PNG]]
 +
 +
 +
''The catalytic triad in Archaeoglobus fulgidus Carboxylesterase is very close to the ligand which is also present in aryformamidase.''
 +
 +
 +
 +
'''Sequence alignment:'''
 +
 +
''Sections of alignment showing the conserved residues across bacterial and eukaryotic species.''
 +
 +
[[Image:Alignment1.jpg]]
 +
 +
 
[[Arylformamidase | Return to the main page...]]
 
[[Arylformamidase | Return to the main page...]]

Latest revision as of 01:35, 10 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

Structure was determined using X-ray diffraction by the Joint Center for Structural Genomics (JCSG). The organism is Silicibacter SP. TM1040 and the protein expression system is Escherichia Coli (vector type: plasmid). The resolution is 1.79 A with R-value of 0.224 and R-free value of 0.270. The closer the R values are to each other, the better the quality of the structure.



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. The chains in the protein of interest exist as individual functional units because in the PDB file it assumes the functional biological molecule as a monomer.

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 archeal.PNG


The secondary structure shows the conservation of the order of different conformation types between the protein of interest and the archaeal carboxylesterases.

Images 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. This catalytic triad is also conserved in the Metagenomic Archea Carboxylesterase (PDB ID 2C7B) and the Archaeoglobus fulgidus Carboxylesterase (PDB ID 1JJI)

From PDB ProteinWorkshop 1.5


Figure: The conserved catalytic triad in Archaeoglobus fulgidus Carboxylesterase (PDB ID 1JJI)


Cat triad 1jji.PNG


The catalytic triad in Archaeoglobus fulgidus Carboxylesterase is very close to the ligand which is also present in aryformamidase.


Sequence alignment:

Sections of alignment showing the conserved residues across bacterial and eukaryotic species.

Alignment1.jpg


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