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Table 1 Predicted function of conserved domains, motifs and specific amino acids in yellow lupine proteins [LlCAD (cinnamyl alcohol dehydrogenase); LlCesA8/LlIRX1 (cellulose synthase A catalytic subunit 8/IRREGULAR XYLEM1); LlCOBL4/IRX6 (COBRA-like4); LlGAUT12/LlIRX8 (galacturonosyltransferase12); LlPG/LlQRT2 (polygalacturonase/ QUARTET2); LlPCS1 (PROMOTION OF CELL SURVIVAL1); LlGA3ox (gibberellin 3-oxidase); LlGA2ox1 (gibberellin 2-oxidase1); LlGAMYB)] based on data published in other plant species

From: Anther dehiscence is regulated by gibberellic acid in yellow lupine (Lupinus luteus L.)

Protein Identified conserved domains/motifs/specific amino acids Predicted functions
LlCAD Alcohol dehydrogenase GroES-like domain Catalytic domain with GroES-like structure [38]
Zinc-binding dehydrogenase domain Catalytic activity, zinc ion binding [38]
Zn-1 (GHExVGxVxxxGxxV) and
Zn-2 (GxxVGxGxxxxxCxxCxxCxxxxxxxC)
binding motifs
Zn-1 catalytic centre and
Zn-2 binding site [39]
Three amino acids C, H, C Define places of catalytic Zn action [40]
Four C residues Structural Zn ligation (Zn-2 structural motif) [40]
G residues (GxGGxG) (so-called Rossmann fold) represent NADPH co-substrate-binding motif G residues for substrate specificity [40]
S 212 Specific NADP(H) binding residue [40]
Many conserved residues: S, Q, L, M, W, V, P, L, F, I Determine substrate ligation [38]
LlCesA8/ LlIRX1 N-terminal region inclusive of a Zn-binding RING motif with a strictly conserved CxxC sequence motif beginning amino acids: CxxCx12FxACxxCxxPxCxxCxExxxxxDxxxCxxC Protein-protein interactions in the CesA complex [41,42,43]
Hypervariable region (VR1) of 117 aa, rich in acidic aa This region is more conserved than was previously thought. The contribution of this region to the overall function of the enzyme is unknown [41, 43]
Two transmembrane domains near the N-terminus (TMH1–2) and six transmembrane domains (TMH3–8) at the C-terminus Transmembrane helixes [44]
Large cytosolic/catalytic central domain (CD = globular domain = soluble domain), which includes the Plant Conserved Region (P-CR) within Conserved Region 1 (CR1), Class Specific Region (CSR) within Variable Region 2 (VR2) and Conserved region 2 (CR2) [41,42,43]
Located in the CD domain A consists of several widely spaced aspartic acid (D) residues - a single D followed by a DxD These residues bind the UDP-glucose substrate. Processive enzymes catalyse the addition of many sugar residues to a growing chain [41, 43]
Located in the CD domain B consists of a third conserved aspartic acid (D) residue and three conserved amino acids QxxRW Part of the catalytic site [41, 43]
LlCOBL4/ LlIRX6 The putative conserved domain characteristic to COBRA superfamily CDD (NCBI)
N-terminal signal peptide with cleavage site Signal peptide cleavage site [45, 46]
The putative cellulose-binding site A carbohydrate-binding module (CBM) [46]
The central Cys-rich (CCVS) motif Highly conserved and characteristic for all COBL proteins [45, 46]
Two conserved consensus N-glycosylation sites Asparagine (N)-linked glycosylation of protein [46]
Locus corresponds to the predicted cleavage ω-site at the C-terminus Glycosylphosphatidylinositol (GPI) modification motif. GPI anchors are added through an amide bond onto the last amino acid residue remaining after cleavage of the ω-site [46]
LlGAUT12/LlIRX8 N-terminal cytoplasmic domain Phyre2
The transmembrane domain Phyre2
The specific glycosyl transferase family 8 (GT8) domain Transfer sugar residues to donor molecules. CDD (NCBI)
The catalytic DxD motif CDD (NCBI)
LlPG/ LlQRT Four typical conserved domains I, II, III and IV The well-conserved positively charged domain IV (RIKT) constitutes a likely candidate for ionic interactions with carboxylate groups present in the substrate [47,48,49]
Three aspartic acids (D) in domains I and II The carboxylate group in aspartic acids in NTD and DD structures (domains I and II, respectively) may be a component of the catalytic site [50]
The histidine residue (H) in domain III Participates in catalytic reaction [51]
A tyrosine (Y) at position 320 Catalytically important in PGs [52]
12 cysteine (C) residues Important to maintain the three-dimensional structure of extracellular proteins and are distributed all along the sequences but with a higher frequency at the C-terminal end [49]
LlPCS1 Two motifs in both N (DTGS) and C (DS/LGT)-terminal ends characteristic for pepsin like aspartic proteases Catalytic motifs (CDD, NCBI)
Two catalytic residues (D) Plays key catalytic roles in the pepsin family and conserved for all family members (CDD, NCBI)
Active site flap ATLS and SSSS An extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates or inhibitors within the active site. It also contributes three residues for substrate specificity (CDD, NCBI)
Pepsin A like plant domain Characteristic for chloroplast nucleoids DNA-binding protease and nucellin, pepsin-like aspartic proteases (CDD, NCBI)
TAXi_N domain; TAXI_C domain
Xylanase inhibitor
The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase (cell-survival processes) (CDD, NCBI)
LlGA3ox Gibberellin 3-β-dioxygenase domain CDD (NCBI) [53]
2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase (Oxy) superfamily domain CDD (NCBI)
The His-x-Asp-(x)n-His (HxD … H) and Arg-x-Ser (RxS) motifs Recruit Fe (II) as a cofactor and co-substrate CDD (NCBI)
LlGA2ox1 Gibberellin 2-β-dioxygenase domain CDD (NCBI)
Domain characteristic for 2-oxoglutarate (2OG)-Fe (II)-dependent oxygenase superfamily CDD (NCBI)
The HxD … H and RxS motifs Amino acid residues presumed to bind Fe2+ at the active site of protein
LlGAMYB R2R3 domain Near the 5′ terminus
Box 1, Box 2, Box 3 domains Distributed throughout the protein
REB1 domain Characteristic for Myb superfamily proteins, including transcription factors and mRNA splicing factors
Myb_DNA-binding domain and SANT (SWI3, ADA2, N-CoR and TFIIIB’) domains DNA-binding domains have been designated using CDD (NCBI)