Arylformamidase: Difference between revisions

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== Abstract ==
[[Image:Pretty protein.PNG|centre|framed|'''Figure 1.''' ''2PBL'']]


== Introduction ==
''by Basma Al Alaiwat, Sebastian Mynott and Thomas Parker''


== Results ==
== Abstract ==


== Discussion ==
2PBL, initially annotated as an arylformamidase, was isolated from ''Silicibacter sp. TM1040'' and its structure determined by the JCSG. Based on structural, functional and evolutionary analysis, we have further characterised 2PBL. It was found to contain a conserved functional region present in A/B-hydrolases of many taxonomic groups. Specifically, it was found to share similar structural and sequence characteristics of the prokaryotic HSL family of esterases. Residues of a probable catalytic triad were identified as Ser137, His242 and Glu215. Further experimental characterisation of 2PBL is required to better understand its function.


== Conclusion ==
== Contents ==


== Methods ==
[[Arylformamidase Introduction|Introduction]]


'''Literature search'''
[[Arylformamidase Results|Results]]


A literature search was performed using the putative annotation ‘arylformamidase’. A paper by Pabarcus et al. 2007 was returned which, ironically, described the arylformamidase from ''Mus Musculus''.
[[Arylformamidase Discussion|Discussion]]


'''Conservation of Catalytic Triad'''
[[Arylformamidase Methods|Methods]]


An alignment of 2pbl and the protein of interest was performed using ClustalX. Default parameters were used. Residues of the catalytic triad were identified from the paper describing it and located in the sequence. Conservation of the residue and the surrounding sequence was observed.
[[Arylformamidase Additional Materials|Additional Materials]]


== Additional Materials ==
[[Arylformamidase References|References]]


'''Presentations'''
== Presentations ==


[[Arylformamidase Sequence & Homology | Sequence & Homology]] - ''Sebastian Mynott''
[[Arylformamidase Sequence & Homology | Sequence & Homology]] - ''Sebastian Mynott''
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[[Arylformamidase Structure | Structure]] - ''Basma Al Alaiwat''
[[Arylformamidase Structure | Structure]] - ''Basma Al Alaiwat''


[[Arylformamidase Function | Function]] - ''Thomas Parker''
[[Arylformamidase Function Slide 1 | Function]] - ''Thomas Parker''
 
'''Links'''
 
[http://www.pdb.org/pdb/explore.do?structureId=2PBL Protein Data Bank Entry for 2PBL]
 
'''FASTA Sequence'''
 
>gi|146387357|pdb|2PBL|A Chain A, Crystal Structure Of Putative Thioesterase (Yp_614486.1) From Silicibacter Sp. Tm1040 At 1.79 A Resolution
GXELDDAYANGAYIEGAADYPPRWAASAEDFRNSLQDRARLNLSYGEGDRHKFDLFLPEGTPVGLFVFVH
GGYWXAFDKSSWSHLAVGALSKGWAVAXPSYELCPEVRISEITQQISQAVTAAAKEIDGPIVLAGHSAGG
HLVARXLDPEVLPEAVGARIRNVVPISPLSDLRPLLRTSXNEKFKXDADAAIAESPVEXQNRYDAKVTVW
VGGAERPAFLDQAIWLVEAWDADHVIAFEKHHFNVIEPLADPESDLVAVITA
 
== References ==
 
''Pabarcus MK, Casida JE.''
'''[http://www.ncbi.nlm.nih.gov/pubmed/15935693?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Cloning, expression, and catalytic triad of recombinant arylformamidase.]'''
Protein Expr Purif. Nov;44(1):39-44.
 
''De Simone G, Menchise V, Manco G, Mandrich L, Sorrentino N, Lang D, Rossi M, Pedone C.''
'''[http://www.ncbi.nlm.nih.gov/pubmed/11846563?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus.]'''
J Mol Biol. 2001 Nov 30;314(3):507-18.
 
''Byun JS, Rhee JK, Kim ND, Yoon J, Kim DU, Koh E, Oh JW, Cho HS.''
'''[http://www.ncbi.nlm.nih.gov/pubmed/17625021?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties.]'''
BMC Struct Biol. 2007 Jul 12;7:47.
 
2-''Effect of arylformamidase (kynurenine formamidase) gene inactivation in mice on enzymatic activity, kynurenine pathway metabolites and phenotype''
  http://www.ncbi.nlm.nih.gov/pubmed/12007602?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_Discovery_RA&linkpos=2&log$=relatedarticles&dbfrom=pubmed

Latest revision as of 03:29, 10 June 2008

Figure 1. 2PBL

by Basma Al Alaiwat, Sebastian Mynott and Thomas Parker

Abstract

2PBL, initially annotated as an arylformamidase, was isolated from Silicibacter sp. TM1040 and its structure determined by the JCSG. Based on structural, functional and evolutionary analysis, we have further characterised 2PBL. It was found to contain a conserved functional region present in A/B-hydrolases of many taxonomic groups. Specifically, it was found to share similar structural and sequence characteristics of the prokaryotic HSL family of esterases. Residues of a probable catalytic triad were identified as Ser137, His242 and Glu215. Further experimental characterisation of 2PBL is required to better understand its function.

Contents

Introduction

Results

Discussion

Methods

Additional Materials

References

Presentations

Sequence & Homology - Sebastian Mynott

Structure - Basma Al Alaiwat

Function - Thomas Parker

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