Arylformamidase Structure

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/

Structure of Arylformamidase

Arylformamidase (Whole Protein)

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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

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

2. Interaction of human arylformamidase (AFMID) with other proteins

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

3. 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)

4. 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)

From PDB ProteinWorkshop 1.5

File:Carboxylase.txt

PDB link title

Note: Chain B not shown

Archaeoglobus fulgidus Carboxylesterase (Chain A ONLY)

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.

5. Secondary structure analysis

PDBSum output for arylformamidase

PDBSUM [1]

Archeon Carboxylesterase secondary structure

From PDBsum

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

Yellow indicates conservation

Blue indicates semi-conservation

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.

From PDB ProteinWorkshop 1.5

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

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