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From Proteopedia

Mutations in palmitoyl thiosterase 1

Mutations in palmitoyl thioesterase 1 (PPT1) can cause three types of disorders: Infantile Neuronal Ceroid Lipofuscinosis (INCL) ([1]), Late Infantile Neuronal Ceroid Lipofuscinosis (LINCL) [2], and Juvenile Neuronal Cerioid Lipofuscinosis (JNCL)[3]. The severity of most of the mutations are dependent upon their location inside the protein with respect to the catalytic triad. “Mutations that affect catalysis or substrate binding or disrupt proper folding of the core result in inactive enzymes and lead to a severe clinical phenotype” Mutations. Other mutations that cause less severe disorders can sometimes retain some residual thioesterase activity. These less severe mutations are believed to have small, local changes in areas of the protein that are far away from the catalytic triad and palmitate binding site. A more detailed explanation of how some of the different disorders arise through mutationsMutations.

INCL

Various mutations have been found in INCL patients ( Hofmann S L, Das A K, Yi W, Lu J-Y, Wisniewski K E. Mol Genet Metab. 1999;66:234–239. [PubMed]Das A K, Becerra C H R, Yi W, Lu J-Y, Siakotos A N, Wisniewski K N, Hofmann S L. J Clin Invest. 1998;102:361–370. [PMC free article] [PubMed]). Most of these mutations are caused by nonsense or missense mutations within close proximity to the catalytic triad. These mutations lead to an inactive PPT1 enzyme as they are predicted to create unfavorable steric, polar, and electrostatic interactions that could disturb the nucleophilic elbow. The nucleophilic elbow is responsible for proper location and orientation of the Ser 115 (part of the catalytic triad link?). Catalytic ability would be greatly reduced if the original position of Ser115 was altered because it must be properly orientated to be activated by His289 (part of the catalytic triad Link?) in order to attack the substrate. One example of mutation such as and give a good depiction of how the increase in size in the mutated amino acids and positive charge on lysine mutation would create steric and polar clashes with the adjacent helices of the binding pocket compared to the which is described in more detail below.

Known INCL Mutations 1. Arg122Trp 2. Phe225Ser 3. Gly118Asp 4. Gly42Gln 5. Tyr109Asp 6. His39Asp 7. Glu184Lys 8. Val181Met (link to other mutations image)

Arg122Trp

The most common mutation that occurs in PPT1 is a single missense mutation of Arg122Trp. is located immediately after the nucleophilic elbow of PPT1. The sidechain of Arg122 has a main function to control the spacing between the αC and α6 helices in this region. This is done by Arg122 having with three adjacent amino acids: Ile205, Asn 206, and Gln205. “ means not only a loss of those three hydrogen bonds but also a steric and polarity mismatch with the surrounding residues” Mutations. These would cause a misfolding of the enzyme’s core and cause it to be trapped in the endoplasmic reticulum which results in no detectable PPT1 activity.

LINCL

LINCl is caused by a mutation in the CLN2 gene which “codes for a lysosomal pepstatin-insensitive acid protease that is deficient in LINCL patients” (Vines D J, Warburton M J. FEBS Lett. 1999;443:131–135. [PubMed]. Mutations that tend to lead to LINCL still disrupt the active site and binding pocket geometry but do not do it to the degree that is seen in INCL. One LINCL mutation is . The acts as a hydrogen bond donor to Ala171 and Ala183 and as a hydrogen bond acceptor from Ile200. It is presumed that the mutation to Glu177 would cause a conformation change of the helices in the area. Ala171 and Ala183 make hydrophobic contact with the palmitate, and so the altered conformation associated with those two amino acids would decrease binding affinity of the palmitate, decreasing the catalytic activity but not to the extent of the mutations seen in INCL.

JNCL

JNCL is caused by a mutation in the CLN3 gene which codes for a lysosomal membrane protein of unknown function (Lerner T J, Boustany R N, Anderson J W, D'Arigo K D, Schlumpf K, Buckler A J, Gusella J F, Haines J L, Kremmidiotis G, Lensink I L, et al. Cell. 1995;82:949–957.). Unlike the mutations that cause INCL and LINCL, mutations that lead to JNCL are located away from the active site and are seen to cause less damage to the overall structure of PPT1. Some of the mutations in JNCL have been noted as retaining a low level of PPT1 activity as the catalytic site is left fairly unperturbed. Mutations associated with JNCl are found in two locations, Thr75Pro with Asp79Gly and . These mutations are predicted to disturb the geometry of α1, increase the flexibility of the region, and alter the antiparallel βsheet motif in βa and βb compared to the .