Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases

Abstract

A bioinformatic search was carried for plant homologues of human serine-threonine protein kinases involved in regulation of cell division and microtubule protein phosphorylation (SLK, PAK6, PAK7, MARK1, MAST2, TTBK1, TTBK2, AURKA, PLK1, PLK4 and PASK). A number of SLK, MAST2 and AURKA plant homologues were identified. The closest identified homologue of human AURKA kinase was a protein of unknown function, A7PY12/GSVIVT00026259001 from Vitis vinifera (herein named as "STALK", Serine-Threonine Aurora-Like Kinase). Analysis of STALK's three-dimensional structure confirmed its relationship to the subgroup of AURKA-like protein kinases.

Figure 1

SLK_HUMAN (a), MAST_HUMAN (b) and STK6_HUMAN (c) kinase domain architecture. S_TKc - catalytic domain of serine/threonine-kinases; S_TK_X - auxiliary S_TKc domain; DUF1908 - domain of unknown function (DUF1908); PDZ (also referred as DHR (Dlg homology region) or GLGF (relatively well conserved tetrapeptide in these domains) - domain found in PSD-95, Dlg and ZO-1/2[74]. These domains help anchor transmembrane proteins to the cytoskeleton and hold together signaling complexes [72].

Figure 2

Catalytic domain alignment of human SLK_HUMAN (Q9H2G2) and putative plant SLK-like proteins. NP_BIND (ATP) - nucleotide phosphate binding region; Binding site (ATP) - ATP binding site; ACT_SITE - proton acceptor; consensus conserved motif in catalytic loop region of the subdomain VIb (animals (red): H-R-D-[LI]-K-[GA]-x-N and A. thaliana (blue): H-[RC]-D-[ILV]-K-x-x-N); consensus conserved motif in activation loop of the subdomain VIII (in animals (red): G-T-P-[YF]-[WY]-M-A-P-E and in A. thaliana (blue): G-[TS]-x-x-[WYF]-[ML]-[AS]-P-E)

Figure 3

Phylogenetic tree constructed for SLK kinase of H. sapiens and its plant homologues.

Figure 4

Catalytic domain alignment of MAST_HUMAN (Q6P0Q8) with its plant homologues. NP_BIND (ATP) - nucleotide phosphate binding region; Binding site (ATP) - ATP binding site; ACT_SITE - proton acceptor; consensus conserved for AGC kinases motif in catalytic loop region of the subdomain VIb (animals (red): [HY]-R-D-[LI]-K-[PL]-[ED]-N and A. thaliana (blue): [HY]-[RY]-D-[LI]-K-P-[ED]-N); consensus conserved for AGC kinases motif in activation loop of the subdomain VIII (in animals (red): G-T-P-[EA]-Y-[IM]-A-P-E and in A. thaliana (blue): G-T-x-D-Y-L-A-P-E)

Figure 5

Phylogenetic tree built for H. sapiens MAST2 kinase and its plant homologues; * - plant homologues containing typical for animal MAST2 kinases auxiliary S_TK_X catalytic S_TK_X domain.

Figure 6

Similarity of H. sapiens MAST2 and potential plant homologues for auxiliary S_TK_X domain, conserved active site Asp-635 and ATP-binding motifs (NP_BIND ATP and Lys-541).

Figure 7

Alignment of human Aurora A and its plant homologues. NP_BIND (ATP) - nucleotide phosphate binding site; Binding site (ATP) - ATP binding site; ACT_SITE - proton acceptor site

Figure 8

Phylogenetic tree of STK6_HUMAN (Aurora A) kinase and its plant homologues demonstrating their phylogenetic relationships. Highlighted are the proteins identified in the paper.

Figure 9

Comparison of the catalytic domain spatial structures of the human protein kinase Aurora A (AURKA, STK6, PDB: 2J4Z) and the protein of unknown function STALK (S_T AURKA LIKE KINASE, UniProt: A7PY12) from V. vinifera. "a" (marked by blue) ATP-binding regions in Aurora A and STALK; "b" (marked by red) is active site; "c", "d" (marked by green) are the most spatially variable regions between the two proteins; phosphorylated Thr residues (287, 288) in the Aurora A are marked by brown. In bold are marked the only discrepancies between the corresponding functionally important residues in Aurora A versus STALK: Asn146↔Arg31, Lys141↔Arg26 in "a"; Thr288↔Thr172 in variable region "c"; Pro297↔Ala181 in the DFGWSxxxxxxxRxTxCGTxDYLPPE motif of the activating loop; Val377↔Ile263 in the D2_type destruction box - Rxx(L/I)xxVxxHPW

Figure 10

Conserved motifs typical for Aurora animal kinases found in STALK protein from V. vinifera: a - activation loop conserved motif and b - D2-type destruction box. Marked are the residues different in both proteins.

Figure 11

Interplay of Plk1, AURKA and BORA in cell cycle based on literature data: adapted from [43,46]and is based on references [29,38,43,44,46,57].