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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 TD domain of showing presence of 7 β-sheets and 7 α-helices in AtHK1 (A) and 5 β-sheets and 7 α-helices in OsHK3b (B).
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Figure 3: Secondary structure topology of TD domain of showing presence of 7 β-sheets and 7 α-helices in AtHK1 (A) and 5 β-sheets and 7 α-helices in OsHK3b (B).

Mentions: In order to model the sensory domain structure of AtHK1 (216 amino acid) and CHASE domain in OsHK3b protein (227 amino acid), BLAST searches were performed against the PDB for proteins with similar sequence and known 3D structures. The BLAST results revealed template structure of Arabidopsis HK 4-sensor domain (3T4J.pdb) as a suitable template for modeling CHASE domain in OsHK3b protein. The target CHASE domain sequence of OsHK3b showed 53% identity with 3T4J, template structure. The template structures possess sensor kinase like secondary structure folds. The BLAST results were unable to capture any possible template for modeling AtHK1 sensory domain sequence. Hence, the AtHK1 sensory domain sequence was modeled using threading approach using CPHmodels server (Nielsen, Lundegaard, Lund, & Petersen, 2010) and EsyPred3D (Lambert, Leonard, De Bolle, & Depiereux, 2002), while CHASE domain of OsHK3b was modeled using comparative modeling approach (see Method) (Supplementary Figure 1). The results obtained from CPH webserver and EsyPred3d consensually identified 3C8C.pdb (crystal structure of Mcp_N and cache domains of methyl-accepting chemotaxis protein from Vibrio cholera) as possible template for modeling the AtHK1 sensory domain sequence. The Ramachandran plot analysis showed that the modeled AtHK1 CHASE domain has 92.9% residues found in most favorable regions with the remaining 6.6% of residues occurring in generously allowed regions, while 0.5% residues were found in disallowed region. While in OsHK3b, CHASE domain has 98.5% residues in most favorable regions with the remaining 0.5% of residues occurring in generously allowed regions, 1.0% of the residues were found in disallowed region (Supplemental Figure 2(A) and (B)). The PROCHECK result summary showed 29 out of 212 residues labeled in CHASE domain structure of AtHK1, while in CHASE domain of OsHK3b, 10 out of 225 residues were found to be labeled. The torsion angles of the side chain designated by χ1–χ2 plots showed 3 labeled residues out of 121 in AtHK1 CHASE domain, while in OsHK3b CHASE domain, 3 out of 133 residues were found labeled. The G-factor score of the AtHK1 CHASE domain was found to be −0.35 for dihedral bonds, −0.55 for covalent bonds, and −0.41 overall, while the OsHK3b CHASE domain model was observed to be −0.04 for dihedral bonds, −0.31 for covalent bonds, and −0.13 overall. The distribution of the main chain bond lengths and bond angles were 96.9% and 86.7% within limits for the modeled AtHK1 CHASE domain. On the other hand, for OsHK3b CHASE domain, main chain bond lengths and bond angles were found to be 98.4 and 91.6% within the limit. The PROSA-web energy plots for CHASE domains of AtHK1 and OsHK3b protein showed z-score for pair, surface and combined energy which was found to be −5.93 and −5.69, respectively (Supplementary Figure 3(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 TD domain of showing presence of 7 β-sheets and 7 α-helices in AtHK1 (A) and 5 β-sheets and 7 α-helices in OsHK3b (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Secondary structure topology of TD domain of showing presence of 7 β-sheets and 7 α-helices in AtHK1 (A) and 5 β-sheets and 7 α-helices in OsHK3b (B).
Mentions: In order to model the sensory domain structure of AtHK1 (216 amino acid) and CHASE domain in OsHK3b protein (227 amino acid), BLAST searches were performed against the PDB for proteins with similar sequence and known 3D structures. The BLAST results revealed template structure of Arabidopsis HK 4-sensor domain (3T4J.pdb) as a suitable template for modeling CHASE domain in OsHK3b protein. The target CHASE domain sequence of OsHK3b showed 53% identity with 3T4J, template structure. The template structures possess sensor kinase like secondary structure folds. The BLAST results were unable to capture any possible template for modeling AtHK1 sensory domain sequence. Hence, the AtHK1 sensory domain sequence was modeled using threading approach using CPHmodels server (Nielsen, Lundegaard, Lund, & Petersen, 2010) and EsyPred3D (Lambert, Leonard, De Bolle, & Depiereux, 2002), while CHASE domain of OsHK3b was modeled using comparative modeling approach (see Method) (Supplementary Figure 1). The results obtained from CPH webserver and EsyPred3d consensually identified 3C8C.pdb (crystal structure of Mcp_N and cache domains of methyl-accepting chemotaxis protein from Vibrio cholera) as possible template for modeling the AtHK1 sensory domain sequence. The Ramachandran plot analysis showed that the modeled AtHK1 CHASE domain has 92.9% residues found in most favorable regions with the remaining 6.6% of residues occurring in generously allowed regions, while 0.5% residues were found in disallowed region. While in OsHK3b, CHASE domain has 98.5% residues in most favorable regions with the remaining 0.5% of residues occurring in generously allowed regions, 1.0% of the residues were found in disallowed region (Supplemental Figure 2(A) and (B)). The PROCHECK result summary showed 29 out of 212 residues labeled in CHASE domain structure of AtHK1, while in CHASE domain of OsHK3b, 10 out of 225 residues were found to be labeled. The torsion angles of the side chain designated by χ1–χ2 plots showed 3 labeled residues out of 121 in AtHK1 CHASE domain, while in OsHK3b CHASE domain, 3 out of 133 residues were found labeled. The G-factor score of the AtHK1 CHASE domain was found to be −0.35 for dihedral bonds, −0.55 for covalent bonds, and −0.41 overall, while the OsHK3b CHASE domain model was observed to be −0.04 for dihedral bonds, −0.31 for covalent bonds, and −0.13 overall. The distribution of the main chain bond lengths and bond angles were 96.9% and 86.7% within limits for the modeled AtHK1 CHASE domain. On the other hand, for OsHK3b CHASE domain, main chain bond lengths and bond angles were found to be 98.4 and 91.6% within the limit. The PROSA-web energy plots for CHASE domains of AtHK1 and OsHK3b protein showed z-score for pair, surface and combined energy which was found to be −5.93 and −5.69, respectively (Supplementary Figure 3(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