Arylformamidase Function: Difference between revisions

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[[Image:Arylformamidase function.jpg]]
== Evidence from Similar Sequences ==


'''Lines of evidence:'''  
The putative annotation which was initially provided ''on the basis of...'' prompted a literature search using the term 'arylformamidase'. Pabarcus et al. (2007) have analysed the function of an arylformamidase present in the liver of ''Mus musculus''.
Ironically, from the BLAST results, the most similar sequence to 2pbl for which there was functional information available was the arylformamidase characterised by Pabarcus et al. 2007. Using site-directed mutagenesis, a catalytic triad was identified - S162, D247 and H279. To elucidate any functional similarity between arylformamidase and 2pbl, conservation of the catalytic triad was assessed through a clustalW alignment (see figure ...). Both S162 and H279 were found to be conserved in relatively conserved regions of the alignment whereas D247 had undergone a semi-conserved substitution. These residues correlated to... The residues were located on the tertiary structure of 2pbl and determined to be sufficiently proximal to one another to permit catalysis (see figure...).


Sequence
[[Image:arylformamidase_alignment.png|centre|framed|'''Figure 3:''' ''Conservation of the catalytic triad between Arylformamidase and 2pbl.'']]


Structural evidence
Arylformamidase forms part of the tryptophan degradation pathway...


Genomic Context
[[Image:Arylformadisae_reaction.gif|centre|framed|'''Figure 4:''' ''The reaction catalysed by Arylformamidase.'']]


Cellular Context (location)  
Carboxylesterases have a common reaction mechanism (see figure ...). This is somewhat similar to the arylformamidase reaction mechanism incorporating hydrolysis of a ... bond.


Species Similarities
[[Image:Carboxylesterase_reaction.gif|centre|framed|'''Figure 2:''' ''The fundamental reaction catalysed by carboxylesterases.'']]


== Literature Evidence ==
Evolutionary...


[[Arylformamidase | Return to the main page...]]
[[Arylformamidase | Return to the main page...]]
Arylformamidase – Functional Analysis
Possible ExPASy entry: 3.5.1.9
Deducing Function
pdb|2PBL|A Chain A, Crystal Structure Of Putative Thioesterase (...  516  e-145 reference
ref|YP_614486.1| putative esterase/lipase/thioesterase [Siliciba...  514  e-144 reference
ref|ZP_01753905.1| possible esterase/lipase/thioesterase [Roseob...  416  e-114 prokaryotic genome pipeline
ref|ZP_02144596.1| putative esterase/lipase/thioesterase [Phaeob...  409  e-112 prokaryotic genome pipeline
ref|ZP_02147804.1| possible esterase/lipase/thioesterase [Phaeob...  408  e-112 prokaryotic genome pipeline
ref|ZP_01055720.1| possible esterase/lipase/thioesterase [Roseob...  396  e-109 prokaryotic genome pipeline
ref|ZP_01441538.1| possible esterase/lipase/thioesterase [Roseov...  318  3e-085 prokaryotic genome pipeline
Initially, an examination of the closest results (E-value < 10e-70) provided no clues towards the protein’s function. The majority of the results were the outcome of the NCBI Prokaryotic Genomes Automatic Annotation Pipeline Group. The automatic annotations returned suggested the sequence represented a putative esterase, lipase or thioesterase. Reason… No functional data or useful associated literature was returned.
A search of PubMed using common terms namely appearing in the annotation of the blast results ‘arylformamidase’ and ‘kynurenine formamidase’ returned some useful literature.
Literature Notes
2005 Pabarcus
Sequence used accession number - NP_082103.1.
E-value from BLAST - 6e-017.
• Function:
o Catalyzes the hydrolysis of N-formyl-L-kynurenine (NFK) to L-kynurenine.
 The second step in the pathway for conversion of tryptophan to nicotinic acid, NAD(H) and NADP(H).
o Assayed through activity for hydrolyzing NFK.
o Current interest in considering organophosphate toxicology.
o Inactivation in mice results in a profound imbalance of metabolites of the kynurenine pathway of tryptophan degradation, which may explain the kidney deterioration and abnormal immune system.
'''Structure:
o An α/β-hydrolase fold is suggested for AFMID based onits primary sequence and predicted secondary structure.
o A three-dimensional model based on the structures of homologous proteins implicates Ser162, Asp247, and His279 as the active site triad.
 Site-directed mutagenesis of catalytic triad residues.'''
Sequence:
o AFMID has been characterized at the nucleotide and/or protein level in Wve species; Saccharomyces cerevisiae, Polaribacter Wlamentus, Gemmata sp. Wal-1, Drosophila melanogaster, and Mususculus with six protein and ten nucleotide sequences found for AFMID using the National Center for Biotechnology Information Entrez search engine.
2005 Casida
• Secondary target conferring toxicity in hen eggs of organophosphorous (OP)-based compounds.
2005 Dobrovolsky
• Afmid knockout experiment.
• Afmid/Tk -deficient mice are known to develop sclerosis of glomeruli and to have an abnormal immune system.
• 13% residual formyl-kynurenine hydrolysis in the kidney of KO mice, suggesting the existence of a formamidase other than Afmid.

Latest revision as of 11:26, 3 June 2008

Evidence from Similar Sequences

The putative annotation which was initially provided on the basis of... prompted a literature search using the term 'arylformamidase'. Pabarcus et al. (2007) have analysed the function of an arylformamidase present in the liver of Mus musculus. Ironically, from the BLAST results, the most similar sequence to 2pbl for which there was functional information available was the arylformamidase characterised by Pabarcus et al. 2007. Using site-directed mutagenesis, a catalytic triad was identified - S162, D247 and H279. To elucidate any functional similarity between arylformamidase and 2pbl, conservation of the catalytic triad was assessed through a clustalW alignment (see figure ...). Both S162 and H279 were found to be conserved in relatively conserved regions of the alignment whereas D247 had undergone a semi-conserved substitution. These residues correlated to... The residues were located on the tertiary structure of 2pbl and determined to be sufficiently proximal to one another to permit catalysis (see figure...).

Figure 3: Conservation of the catalytic triad between Arylformamidase and 2pbl.

Arylformamidase forms part of the tryptophan degradation pathway...

Figure 4: The reaction catalysed by Arylformamidase.

Carboxylesterases have a common reaction mechanism (see figure ...). This is somewhat similar to the arylformamidase reaction mechanism incorporating hydrolysis of a ... bond.

Figure 2: The fundamental reaction catalysed by carboxylesterases.

Evolutionary...

Return to the main page...

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