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. 2019 Aug 1;20:172. doi: 10.1186/s12931-019-1146-3

Table 1.

Protein structure prediction results for the two GSTCD isoforms using three models I-TASSER, SWISS- MODEL and Phyre2. Methyltransferase (MTF) enzymes are frequently found in the top 3 structural templates listed for each server and the top 50 template results in SWISS-MODEL were entirely methyltransferase proteins, with specific focus on rRNA methyltransferase function. Alternatively, I-TASSER identified homology in this region with transport receptors, specifically importin β subunit 1, involved in transporting proteins into the nucleus [25]. Other top hits included: exodeoxyribonuclease (catalyses degradation of double stranded DNA), Ras guanyl-releasing protein 1 (nucleotide exchange factor specifically activating Ras, activates the extracellular signal-regulated kinases/mitogen-activated protein kinase (ERK/MAPK) cascade) and nicotinamide adenine dinucleotide binding (NADB)-Rossmann fold superfamily protein (structural motif found in proteins that bind nucleotides)

Protein Structure Results I-TASSER SWISS-MODEL Phyre2
Variant 1 Variant 2 Variant 1 Variant 2 Variant 1 Variant 2
Predicted Secondary Structure

Primarily α-helices with intermittent coil structures.

β-strands only present at termini.

N/A

Primarily intermittent α-helices (45%).

β-strands only present at termini (12%).

Two predicted transmembrane regions (30-40aa and 281-299aa).

Primarily intermittent α-helices (55%).

β-strands only present at termini (10%).

Two predicted transmembrane regions (29-38aa and 194-212aa).

Regions of Primary Sequence Homology

Primarily across the MTF domain to C-terminus.

Partial matches across whole protein.

Only across the MTF domain to C-terminus Only across the MTF domain
Intrinsic disorder N/A Low disorder across C-terminus High disorder across C-terminus Two theoretical central regions of disorder (27%):• 204-270aa• 325-386aa Two theoretical central regions of disorder (26%):• 118-184aa• 257-299aa
Top 3 Structural Templates

Putative MTF

Importin β subunit

Exodeoxyribonuclease

Ras guanyl-releasing protein 1

MTF

Protein RdmB MTF

Protein RdmB MTF

Protein RdmB MTF

Putative rRNA methylase

Putative rRNA methylase

rRNA small subunit MTF

rRNA small subunit MTF

Transferase

S-adenosyl-L-methionine-dependent MTF

Transferase

NADB-Rossmann fold superfamily protein

S-adenosyl-L-methionine-dependent MTF