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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.)


Identified conserved domains/motifs/specific amino acids

Predicted functions


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)


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]


The putative conserved domain characteristic to COBRA superfamily


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]


N-terminal cytoplasmic domain


The transmembrane domain


The specific glycosyl transferase family 8 (GT8) domain

Transfer sugar residues to donor molecules. CDD (NCBI)

The catalytic DxD motif



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]


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)


Gibberellin 3-β-dioxygenase domain

CDD (NCBI) [53]

2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase (Oxy) superfamily domain


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)


Gibberellin 2-β-dioxygenase domain


Domain characteristic for 2-oxoglutarate (2OG)-Fe (II)-dependent oxygenase superfamily


The HxD … H and RxS motifs

Amino acid residues presumed to bind Fe2+ at the active site of protein


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)