Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences.

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Date: Mar. 1, 2021
From: BMC Research Notes(Vol. 14, Issue 1)
Publisher: BioMed Central Ltd.
Document Type: Report
Length: 2,927 words
Lexile Measure: 1480L

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Abstract :

Objective Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results This work reports the implementation of [formula omitted], a web server with dual functionality and an extension of previous work on i2OGdd enzymes [formula omitted]. [formula omitted], in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. [formula omitted], utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. [formula omitted], also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. [formula omitted], is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG. Keywords: Facial triad, Hidden markov model, Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases

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Gale Document Number: GALE|A655220853