Difference between revisions of "Arylformamidase Structure"

From MDWiki
Jump to navigationJump to search
Line 6: Line 6:
[[Image:Whole protein.png]]
[[Image:Arylformamidase the whole protein.PNG]]
Line 153: Line 154:
GLU 214
GLU 214
The unknown ligand is shown protruding from a groove and kinda neatly fits in the pocket.
The unknown ligand is shown protruding from a groove and neatly fits in a pocket.
[[Arylformamidase | Return to the main page...]]
[[Arylformamidase | Return to the main page...]]

Revision as of 06:07, 30 May 2008

1. Structure of Arylformamidase


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. Those chains exist as indivitual functional units.

Chain A of arylformamidase

Chain A.jpg

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.

2. Putative Thioesterase

Thioesterases split ester groups into acid and alcohol in the presence of water, specifically at a thiol group.

Thioesterases or thiolester hydrolases are members of E.C.3.1.2.

Our structure resembles carboxylesterases (hydrolases) hence it is predicted that it has similar cellular activity.

3. 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

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


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)



Metagenomic Archea Carboxylesterase A chain

Carboxylase A chain.PNG


PDB link title

Archaeoglobus fulgidus Carboxylesterase (Chains A B C D)

Archeaon Carboxylesterase.PNG

File:Carboxylesterase (archaeon).txt

PDB link title

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

PDBSum output for arylformamidase



Archeon Carboxylesterase secondary structure


6. The conservation of the ser/his/asp catalytic triad

Catalytic triad conversation.PNG

Yellow indicates conservation

Blue indicates semi-conservation


This image shows the triad conserved residues in our protein

SER 136

HIS 241

GLU 214

The unknown ligand is shown protruding from a groove and neatly fits in a pocket.

Return to the main page...