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Putative osmosensor--OsHK3b--a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis.

Kushwaha HR, Singla-Pareek SL, Pareek A - J. Biomol. Struct. Dyn. (2013)

Bottom Line: Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2.The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved.Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction.

View Article: PubMed Central - PubMed

Affiliation: a Synthetic Biology and Biofuel Group , International Center for Genetic Engineering and Biotechnology , New Delhi 110067 , India .

ABSTRACT
Prokaryotes and eukaryotes respond to various environmental stimuli using the two-component system (TCS). Essentially, it consists of membrane-bound histidine kinase (HK) which senses the stimuli and further transfers the signal to the response regulator, which in turn, regulates expression of various target genes. Recently, sequence-based genome wide analysis has been carried out in Arabidopsis and rice to identify all the putative members of TCS family. One of the members of this family i.e. AtHK1, (a putative osmosensor, hybrid-type sensory histidine kinase) is known to interact with AtHPt1 (phosphotransfer proteins) in Arabidopsis. Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2. The analysis of amino acid sequence of AtHK1 showed the presence of transmitter domain (TD) and receiver domain (RD), while OsHK3b showed presence of three conserved domains namely CHASE (signaling domain), TD, and RD. In order to elaborate on structural details of functional domains of hybrid-type HK and phosphotransfer proteins in both these genera, we have modeled them using homology modeling approach. The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved. Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction.

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Secondary structure topology of HPt protein showing the presence of 7 α-helices in Arabidopsis (AtHPt1) (A) and 6 α-helices in O. sativa (OsHPt2) (B).
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Figure 7: Secondary structure topology of HPt protein showing the presence of 7 α-helices in Arabidopsis (AtHPt1) (A) and 6 α-helices in O. sativa (OsHPt2) (B).

Mentions: To create a model of RD of AtHK1 and OsHK3b protein, searches were made against PDB database using BLAST for proteins with similar sequence and known 3D structures using the 162 amino acid and 132 amino acid domain sequences, respectively. The search resulted in identification of structures of RR in Arabidopsis (3MM4.pdb, RD of HK, CKI1 and 3MMN.pdb, RD of HK, CKI1 with Mg2+), and Saccharomyces cerevisiae (1OXB.pdb, YPD1 and SLN1 complex), as possible templates for modeling RD of AtHK1 and OsHK3b protein (Supplementary Figure 7(A) and (B)). The target sequence of RD in AtHK1 showed 32, 32, and 30% identity with template structures 3MM4, 3MMN, and 1OXB, respectively, while the target sequence of RD in OsHK3b showed 37, 37, and 34% identity with the template structures 3MM4, 3MMN, and 1OXB, respectively. Ramachandran plot for the modeled RD structure of AtHK1 showed 97.3% residues in allowed region, 1.4% in generously allowed region, and only 1.4% in disallowed region, while the modeled RD of OsHK3b showed 96.5% residues in allowed region, 2.6% in generously allowed regions, and only 0.9% in disallowed region (Supplemental Figure 8(A) and (B)). The PROCHECK result summary showed 7 out of 160 residues labeled in RD for AtHK1, while for that of OsHK3b, 8 residues out of 130 were labeled. The torsion angles of the side chain designated by χ1–χ2 plots showed 3 labeled residues out of 92 in RD for AtHK1, it was found to be 2 out of 82 residues in case of RD structure of OsHK3b. The G-factor scores of the model were −0.03 for dihedral bonds, −0.34 for covalent bonds, and −0.14 overall in RD structure in AtHK1, while in the model of RD in OsHK3b, the observed G-factor scores were 0.06 for dihedral bonds, −0.29 for covalent bonds, and −0.07 overall. The distribution of the main chain bond lengths and bond angles were 98.9 and 90.9% within limits for RD in AtHK1 and 98.5 and 90.8% within the limit for RD model of OsHK3b. The PROSA-web energy plots for RD of AtHK1 and OsHK3b showed a z-score for pair, surface and combined energy was found to be −3.97 and −4.42, respectively (Supplemental Figure 9(A) and (B)).


Putative osmosensor--OsHK3b--a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis.

Kushwaha HR, Singla-Pareek SL, Pareek A - J. Biomol. Struct. Dyn. (2013)

Secondary structure topology of HPt protein showing the presence of 7 α-helices in Arabidopsis (AtHPt1) (A) and 6 α-helices in O. sativa (OsHPt2) (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4017273&req=5

Figure 7: Secondary structure topology of HPt protein showing the presence of 7 α-helices in Arabidopsis (AtHPt1) (A) and 6 α-helices in O. sativa (OsHPt2) (B).
Mentions: To create a model of RD of AtHK1 and OsHK3b protein, searches were made against PDB database using BLAST for proteins with similar sequence and known 3D structures using the 162 amino acid and 132 amino acid domain sequences, respectively. The search resulted in identification of structures of RR in Arabidopsis (3MM4.pdb, RD of HK, CKI1 and 3MMN.pdb, RD of HK, CKI1 with Mg2+), and Saccharomyces cerevisiae (1OXB.pdb, YPD1 and SLN1 complex), as possible templates for modeling RD of AtHK1 and OsHK3b protein (Supplementary Figure 7(A) and (B)). The target sequence of RD in AtHK1 showed 32, 32, and 30% identity with template structures 3MM4, 3MMN, and 1OXB, respectively, while the target sequence of RD in OsHK3b showed 37, 37, and 34% identity with the template structures 3MM4, 3MMN, and 1OXB, respectively. Ramachandran plot for the modeled RD structure of AtHK1 showed 97.3% residues in allowed region, 1.4% in generously allowed region, and only 1.4% in disallowed region, while the modeled RD of OsHK3b showed 96.5% residues in allowed region, 2.6% in generously allowed regions, and only 0.9% in disallowed region (Supplemental Figure 8(A) and (B)). The PROCHECK result summary showed 7 out of 160 residues labeled in RD for AtHK1, while for that of OsHK3b, 8 residues out of 130 were labeled. The torsion angles of the side chain designated by χ1–χ2 plots showed 3 labeled residues out of 92 in RD for AtHK1, it was found to be 2 out of 82 residues in case of RD structure of OsHK3b. The G-factor scores of the model were −0.03 for dihedral bonds, −0.34 for covalent bonds, and −0.14 overall in RD structure in AtHK1, while in the model of RD in OsHK3b, the observed G-factor scores were 0.06 for dihedral bonds, −0.29 for covalent bonds, and −0.07 overall. The distribution of the main chain bond lengths and bond angles were 98.9 and 90.9% within limits for RD in AtHK1 and 98.5 and 90.8% within the limit for RD model of OsHK3b. The PROSA-web energy plots for RD of AtHK1 and OsHK3b showed a z-score for pair, surface and combined energy was found to be −3.97 and −4.42, respectively (Supplemental Figure 9(A) and (B)).

Bottom Line: Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2.The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved.Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction.

View Article: PubMed Central - PubMed

Affiliation: a Synthetic Biology and Biofuel Group , International Center for Genetic Engineering and Biotechnology , New Delhi 110067 , India .

ABSTRACT
Prokaryotes and eukaryotes respond to various environmental stimuli using the two-component system (TCS). Essentially, it consists of membrane-bound histidine kinase (HK) which senses the stimuli and further transfers the signal to the response regulator, which in turn, regulates expression of various target genes. Recently, sequence-based genome wide analysis has been carried out in Arabidopsis and rice to identify all the putative members of TCS family. One of the members of this family i.e. AtHK1, (a putative osmosensor, hybrid-type sensory histidine kinase) is known to interact with AtHPt1 (phosphotransfer proteins) in Arabidopsis. Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2. The analysis of amino acid sequence of AtHK1 showed the presence of transmitter domain (TD) and receiver domain (RD), while OsHK3b showed presence of three conserved domains namely CHASE (signaling domain), TD, and RD. In order to elaborate on structural details of functional domains of hybrid-type HK and phosphotransfer proteins in both these genera, we have modeled them using homology modeling approach. The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved. Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction.

Show MeSH