Solanum lycopersicum ACC Synthase

Amanda He '16 and Andrew Pearlman '15

Contents:

I. Introduction

1-aminoacyclopropane 1-carboxylate synthase (ACC synthase) is an enzyme that plays a significant role in synthesizing ethylene, a plant hormone produced in a variety of higher plants [1]. Ethylene is an important hormone for ripening and germination processes.  Ethylene biosynthesis consists of three main steps. In the second step, ACC synthase catalyzes the cyclization of the S-adenosy-L-methionine (SAM), which produces 5'-methylthioadenosine and ACC. This step is the rate-limiting step in ethylene synthesis [2].
 
In order for ACC synthase to function, it requires the cofactor, pyridoxal-5'-phosphate (PLP). PLP has been found to activate catalysis in enzymes, including ACC synthase, by binding to the substrate active site.

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II. General Structure

The tomato ACC synthase monomer has two , an alpha-beta-alpha sandwich domain and an alpha-beta domain. The alpha-beta-alpha sandwich domain has a central seven-strand beta-sheet that is flanked between nine alpha-helices [button of beta sheet]. The alpha-beta domain has five beta-strands and five alpha-helices 

ACC synthase typically appears in a dimeric form as do most PLP-dependent enzymes. However, there is not a substantial difference between the functionality of the monomer and dimer forms because there were not a significant difference in conformational change between the two when the inhibitor, AVG, binded [3].

CAP is a dimer of 22, 500 molecular weight, composed of two chemically identical polypeptide chains each 209 amino acids in length.

The overall structure of the dimer is assymetric; one subunit adopts a "closed" conformation in which the amino- and carboxy-termini are closer together than in the more "open" subunit. Each subunit is composed of two distinct domains connected by a hinge region. The N-terminal domain is responsible for dimerization and cAMP binding. The carboxy-terminal domain contains a helix-turn helix DNA binding motif, and is also responsible for DNA bending. 

III. Cofactor PLP Binding

ACC synthase forms a complex with cofactor, pyridoxal-5'-phosphate (PLP) in order to be able to catalysis its substrate, S-adenosylmethionine (SAM). PLP is an active form of vitamin B6 that is able to catalyze reactions by forming a covalent bond. In the case of ACC synthase, PLP forms a covalent bond to [Lys 278]


In ACC synthase's dimeric form, the active site for substrate binding is dually occupied by PLP and the substrate, SAM.

The nitrogen atom of PLP forms a [hydrogen bond] with Asp 237 of the ACC synthase. Since aspartate is negatively charged, it is able to stabilize the protonation state of the pyridine nitrogen [3].


An important recognition site for cAMP within CAP is the ionic bond formed between the side chain of Arg-82 and the negatively charged phosphate group of cAMP. In the crystal structure, the two cAMP molecules are buried deep within the beta roll and the C-helix.

PLP 


It is unclear how cAMP enters or leaves the binding site, but this probably requires the separation of the two subunits of the dimer, or the movement of the beta roll and the C helix away from each other. Other side-chain interactions between the protein and cAMP are hydrogen bonds occuring at Thr-127, Ser-128, Ser-83, and Glu-72. Additional hydrogen bonding between is seen between cAMP and the polypeptide backbone at residues 83 and 71

IV. Inhibitor AVG Binding

Workers in the agricultural industry are familiarized with working with aminoethoxyvinylglycine (AVG), a naturally produced amino acid that has a role in inhibition of ethylene biosynthesis [5]. AVG is a competitive inhibitor of ACC synthase. 

AVG binds to a location neighboring the cofactor, PLP. The alpha-carboxylate group of AVG forms three hydrogen bonds with PLP at [Ala 54], [Arg 412], and water. Additionally, AVG forms a van der Waals contact with [Tyr 152]. All these sites are highly conserved because they are also the sites at which the substrate, SAM would interact with to bind.


Once CAP has bound cAMP, it is ready to bind to the DNA. Binding occurs at the conserved sequence of 5'-AAATGTAGATCACATTT-3' Hydrogen bonds between the protein and the DNA phsophates occur at the backbone amide of residue 139, and the side chains of Thr-140, Ser-179, and Thr-182 In addition to these phosphate interactions, the side chains of Glu-181 and Arg-185, both emanating from the recognition helix directly contact the bases within the major groove of the DNA. Because of the way that the protein binds to the DNA, a kink of ~40 degrees occurs between nucleotide base pairs six and seven on each side of the dyad axis, 5'-TG-3' This sequence has been shown to favor DNA flexibility and bending in other systems as well. Because of this kink, an additional five ionic interactions and four hydrogen bonds are able to occur between the protein and the DNA strand. Examples of these new interactions occur between Lys-26, Lys-166, His-199 and the DNA sugar-phosphate backbone The DNA bend is integral to the mechanism of transcription activation. Not only does it place CAP in the proper orientation for interaction with RNA polymerase, but wrapping the DNA around the protein may result in direct contacts between upstream DNA and RNA polymerase. 

V. Activating Regions

Transcription activation by CAP requires more than merely the binding of cAMP and binding and bending of DNA. CAP contains an "activating region" that has been proposed to participate in direct protein-protein interactions with RNA polymerase and/or other basal transcription factors. Specifically, amino acids 156, 158, 159, and 162 have been proposed to be critical for transcription activation by CAP. These amino acids are part of a surface loop composed of residues 152-166 Researchers have concluded that the third and final step in transcription activation is this direct protein-protein contact between amino acids 156-162 of CAP, and RNA polymerase.


VI. References
  1. Zhang, Z., Ren, J., Clifton, I.J., and Schofield, C.J. 2004. Crystal Structure and Mechanistic Implications of 1-aminocyclopropane-1-carboxylic acid oxidase - the ethylene forming enzyme. Cell. 11(10): 1383-1394.
  2. Yip, W., Moore, T., and Yang, S.F. 1992. Differential accumulation of transcripts for four tomato 1-aminocyclopropane-1-carboxylate synthase homologs under various conditions. Proc. Natl. Acad. Sci. 89: 2475-2479.
  3. Huai, Q., Xia, Y., Chen, Y., Callahan, B., Li, N., and Ke, H. 2001. Crystal structures of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with aminoethoxyvinylglycine and pyridoxal-5'-phosphate provide new insight into catalytic mechanisms. The Journal of Biological Chemistry. 276(41): 38210-38216.
  4. Kiberb, J. "The
  5. Nakatsuka, A., Murachi, S., Okunishi, H., Shiomi, S., Nakano, R., Kubo, Y., and Inaba, A. 1998. Differential expression and internal feedback regulation of 1-aminocyclopropane-1-carboxylate synthase, 1-aminocyclopropane-1-carboxylate oxidase, and ethylene receptor genes in tomato fruit during development and ripening. Plant Physiology. 118: 1295-1305.
  6. Rath, A.C., Kang, I., Park, C., Yoo, W., and Byun, J. 2006. Foliar application of aminoethoxyvinylglycine (AVG) delays fruit ripening and reduces pre-harvest fruit drop and ethylene production of bagged "Kogetsu" apples. Plant Growth Regul. 50: 91-100.
  7. Saltveit, M.E. 2004. Aminoethoxyvinylglycine (AVG) reduces ethylene and protein biosynthesis in excised discs of mature-green tomato pericarp tissue. Postharvest Biology and Technology. 35: 183-190.

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