| Literature DB >> 31850369 |
Oziniel Ruzvidzo1, Chris Gehring2, Aloysius Wong3.
Abstract
It is increasingly clear that plant genomes encode numerous complex multidomain proteins that harbor functional adenylyl cyclase (AC) centers. These AC containing proteins have well-documented roles in development and responses to the environment. However, it is only for a few of these proteins that we are beginning to understand the intramolecular mechanisms that govern their cellular and biological functions, as detailed characterizations are biochemically and structurally challenging given that these poorly conserved AC centers typically constitute only a small fraction (<10%) of complex plant proteins. Here, we offer fresh perspectives on their seemingly cryptic activities specifically showing evidence for the presence of multiple functional AC centers in a single protein and linking their catalytic strengths to the Mg2+/Mn2+-binding amino acids. We used a previously described computational approach to identify candidate multidomain proteins from Arabidopsis thaliana that contain multiple AC centers and show, using an Arabidopsis leucine-rich repeat containing protein (TAIR ID: At3g14460; AtLRRAC1) as example, biochemical evidence for multienzymatic activities. Importantly, all AC-containing fragments of this protein can complement the AC-deficient mutant cyaA in Escherichia coli, while structural modeling coupled with molecular docking simulations supports catalytic feasibility albeit to varying degrees as determined by the frequency of suitable substrate binding poses predicted for the AC sites. This statistic correlates well with the enzymatic assays, which implied that the greatly reduced AC activities is due to the absence of the negatively charged [DE] amino acids previously assigned to cation-, in particular Mg2+/Mn2+-binding roles in ACs.Entities:
Keywords: Arabidopsis thaliana; adenylyl cyclase; cAMP; leucine-rich repeat; multidomain proteins; multiple AC centers
Year: 2019 PMID: 31850369 PMCID: PMC6901789 DOI: 10.3389/fmolb.2019.00136
Source DB: PubMed Journal: Front Mol Biosci ISSN: 2296-889X
Figure 1Computational identification of proteins with multiple adenylyl cyclase (AC) centers in Arabidopsis thaliana and functional characterizations of AtLRRAC1 AC catalytic centers. (A) Alignment of the AC catalytic centers of proteins with multiple AC centers in Arabidopsis thaliana. Asterisks denote AC centers previously confirmed to be catalytically active; *AtLRRAC1 (Ruzvidzo et al., 2013), **AtPPR-AC (Bianchet et al., 2019), and ***AtDGK4 albeit with extraordinarily high recombinant proteins used in the enzymatic assay (Dias et al., 2019). Inset: The 14-amino-acid AC search motif derived from annotated and experimentally tested guanylyl cyclases (GCs) and ACs catalytic centers. The residue forming hydrogen bonding with the purine at position 1 is highlighted in red, the residue conferring substrate specificity in position 3 is highlighted in blue, while the amino acid in position 14 that stabilizes the transition state from ATP to cyclic adenosine monophosphate (cAMP) is highlighted in red. The [DE] amino acid at one to three residues downstream from position 14 participates in Mg2+/Mn2+ binding and is colored green (Gehring, 2010). (B) Cyclic AMP generated by 5 μg of the AtLRRAC148−205, AtLRRAC1234−390, AtLRRAC1426−583, and AtLRRAC11210−1365 recombinant proteins in the presence (at final concentrations) of 1 mM ATP or GTP, or 1 mM ATP and 250 μM Ca2+ when 5 mM Mn2+ ion is the cofactor (control reaction contained all other components except the protein and Ca2+). Insets: Coomassie brilliant blue-stained gels after resolution of the affinity-purified His-tagged recombinant AtLRRAC1 proteins (arrows) by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Data are mean values (n = 3), and error bars show SE of the mean. Asterisks denote values significantly different from those of the control (P < 0.05) as is determined by ANOVA and the post hoc Student–Newman–Keuls multiple range tests. (C) Complementation of cyaA mutation by the AC centers of AtLRRAC1. Recombinant AtLRRAC148−205, AtLRRAC1234−390, AtLRRAC1426−583, and AtLRRAC11210−1365 proteins harboring the four AC centers of AtLRRAC1 complemented the cyaA SP850 mutant E. coli in lactose metabolism (Shah and Peterkofsky, 1991) as indicated by the growth of deep red colonies on MacConkey agar compared to the noncomplemented cyaA mutants that yielded yellowish colonies.
Figure 2Computational assessment of the adenylyl cyclase (AC) centers of AtLRRAC1. (A) Representative images of the four AC-containing fragments of AtLRRAC1 (AtLRRAC148−205, AtLRRAC1234−390, AtLRRAC1426−583, and AtLRRAC11210−1365) docked with ATP are shown as AC1, AC2, AC3, and AC4, respectively. The interaction of ATP with key residues at the AC catalytic centers of each fragment is shown as surface (left panel) and ribbon models (right panel), respectively. The amino acid residues at positions 1 and 14 of the AC centers, which are implicated in interactions with ATP, are colored according to their charges in the surface models and shown as individual atoms in the ribbon models. AC centers are colored orange, and black arrows in the surface models of AtLRRAC1234−390 and AtLRRAC1426−583 show the far distance between ATP and the key amino acids in the AC centers than in AtLRRAC148−205 and AtLRRAC11210−1365. Full-length AtLRRAC1 model was generated using the iterative threading assembly refinement (I-TASSER) method on the online server: http://zhanglab.ccmb.med.umich.edu/I-TASSER/ (Zhang, 2008), and ATP docking simulations were performed using AutoDock Vina (ver. 1.1.2) (Trott and Olson, 2010). Molecular graphics and analyses were performed with the UCSF Chimera package (Pettersen et al., 2004). (B) Frequency of favorable ATP binding pose at the AC centers of AtLRRAC1 as estimated by molecular docking. All four AC-containing fragments of the AtLRRAC1 (AtLRRAC148−205, AtLRRAC1234−390, AtLRRAC1426−583, and AtLRRAC11210−1365) were docked with ATP at their AC centers, and a total of 18 solutions generated by AutoDock Vina (ver. 1.1.2) (Trott and Olson, 2010) for each fragment were then evaluated and expressed as percentage. All clusters, docking data, and interpretation of docking solutions are provided in Supplementary Figure 2. Orientations and binding poses were analyzed with the UCSF Chimera package (Pettersen et al., 2004). Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).