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 | |
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) | ||
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 | ||
LlCOBL4/ LlIRX6 | The putative conserved domain characteristic to COBRA superfamily | CDD (NCBI) |
N-terminal signal peptide with cleavage site | ||
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) |