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BMC Struct Biol
2003 Nov 11;3:8. doi: 10.1186/1472-6807-3-8.
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A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases.
Wlodawer A
,
Durell SR
,
Li M
,
Oyama H
,
Oda K
,
Dunn BM
.
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BACKGROUND: Tripeptidyl-peptidase I, also known as CLN2, is a member of the family of sedolisins (serine-carboxyl peptidases). In humans, defects in expression of this enzyme lead to a fatal neurodegenerative disease, classical late-infantile neuronal ceroid lipofuscinosis. Similar enzymes have been found in the genomic sequences of several species, but neither systematic analyses of their distribution nor modeling of their structures have been previously attempted.
RESULTS: We have analyzed the presence of orthologs of human CLN2 in the genomic sequences of a number of eukaryotic species. Enzymes with sequences sharing over 80% identity have been found in the genomes of macaque, mouse, rat, dog, and cow. Closely related, although clearly distinct, enzymes are present in fish (fugu and zebra), as well as in frogs (Xenopus tropicalis). A three-dimensional model of human CLN2 was built based mainly on the homology with Pseudomonas sp. 101 sedolisin.
CONCLUSION: CLN2 is very highly conserved and widely distributed among higher organisms and may play an important role in their life cycles. The model presented here indicates a very open and accessible active site that is almost completely conserved among all known CLN2 enzymes. This result is somehow surprising for a tripeptidase where the presence of a more constrained binding pocket was anticipated. This structural model should be useful in the search for the physiological substrates of these enzymes and in the design of more specific inhibitors of CLN2.
Figure 1. Sequence comparisons of mammalian CLN2-like enzymes.These sequences correspond to the complete enzymes, including the prosegment. Residues forming the active site are shown in yellow on red background, other conserved residues identified as important for the stability of the enzyme are marked with yellow background, residues identical in at least 5 of the structures are green, and residues similar in their character are shown in magenta. The maturation cleavage point generating the N terminus of the active enzyme is marked with black triangles.
Figure 2. Corrected gene sequence of the zebrafish CLN2.This putative sequence shows the manual corrections that bring it into alignment with the sequence of the fugu enzyme. Inserted nucleotides are marked in green and a deleted one in red.
Figure 3. Sequences of the catalytic domains of CLN2. Complete sequences are shown for CLN2 from human, fugu, and zebrafish, together with the partial sequence of putative CLN2 in Xenopus tropicalis. Residues identical in all four enzymes are colored green and those similar are colored magenta. Active site residues are marked as in Figure 1.
Figure 4. Sequence alignment of bacterial and mammalian enzymes. Alignment of the sequences of sedolisin, kumamolisin, and human CLN2 used in the construction of the model of the latter enzyme. The colors scheme is the same as in Figure 2.
Figure 5. A homology-derived model of human CLN2. Ribbon diagram of the Cα trace of CLN2, with the segments that were modeled based on the highly conserved core of sedolisin and kumamolisin (r.m.s. deviation of 1 Å) colored in red. Side chains of the residues that were found to be mutated in the genes of families of patients with late-infantile neuronal ceroid lipofuscinosis [17] are marked in ball-and-stick.
Figure 6. A model of the active site of human CLN2. The enzyme is shown in complex with pseudo-iodotyrostatin, a good inhibitor of the sedolisin family of peptidases. Only selected residues of the enzyme are explicitly shown on the background consisting of the molecular surface. The stick model of the inhibitor is colored gold and the P1-P3 residues are labeled in black. Similar views have been previously published for the experimentally-determined structures of sedolisin and kumamolisin [8]. The figure was prepared using the program DINO .
Altschul,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
1997, Pubmed
Altschul,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
1997,
Pubmed
Anand,
Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs.
2003,
Pubmed
Benson,
GenBank.
2002,
Pubmed
Berman,
The Protein Data Bank.
2000,
Pubmed
Bernardini,
Lysosomal degradation of cholecystokinin-(29-33)-amide in mouse brain is dependent on tripeptidyl peptidase-I: implications for the degradation and storage of peptides in classical late-infantile neuronal ceroid lipofuscinosis.
2002,
Pubmed
Comellas-Bigler,
The 1.4 a crystal structure of kumamolysin: a thermostable serine-carboxyl-type proteinase.
2002,
Pubmed
ELLIS,
Studies on the serial extraction of pituitary proteins.
1961,
Pubmed
Ezaki,
Tripeptidyl peptidase I, the late infantile neuronal ceroid lipofuscinosis gene product, initiates the lysosomal degradation of subunit c of ATP synthase.
2000,
Pubmed
Guex,
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
1997,
Pubmed
Katz,
Mouse gene knockout models for the CLN2 and CLN3 forms of ceroid lipofuscinosis.
2001,
Pubmed
Lee,
Aorsin, a novel serine proteinase with trypsin-like specificity at acidic pH.
2003,
Pubmed
Lin,
The human CLN2 protein/tripeptidyl-peptidase I is a serine protease that autoactivates at acidic pH.
2001,
Pubmed
McDonald,
Partial purification and characterization of an ovarian tripeptidyl peptidase: a lysosomal exopeptidase that sequentially releases collagen-related (Gly-Pro-X) triplets.
1985,
Pubmed
Nishii,
Structural and enzymatic characterization of physarolisin (formerly physaropepsin) proves that it is a unique serine-carboxyl proteinase.
2003,
Pubmed
Park,
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
1998,
Pubmed
Rawlings,
Tripeptidyl-peptidase I is apparently the CLN2 protein absent in classical late-infantile neuronal ceroid lipofuscinosis.
1999,
Pubmed
Schechter,
On the size of the active site in proteases. I. Papain.
1967,
Pubmed
Sleat,
Association of mutations in a lysosomal protein with classical late-infantile neuronal ceroid lipofuscinosis.
1997,
Pubmed
Sleat,
Mutational analysis of the defective protease in classic late-infantile neuronal ceroid lipofuscinosis, a neurodegenerative lysosomal storage disorder.
1999,
Pubmed
Thompson,
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
1997,
Pubmed
Tsuruoka,
Collagenolytic serine-carboxyl proteinase from Alicyclobacillus sendaiensis strain NTAP-1: purification, characterization, gene cloning, and heterologous expression.
2003,
Pubmed
Vines,
Purification and characterisation of a tripeptidyl aminopeptidase I from rat spleen.
1998,
Pubmed
Warburton,
The specificity of lysosomal tripeptidyl peptidase-I determined by its action on angiotensin-II analogues.
2001,
Pubmed
Waterston,
Initial sequencing and comparative analysis of the mouse genome.
2002,
Pubmed
Weber,
Molecular modeling of the HIV-1 protease and its substrate binding site.
1989,
Pubmed
Wlodawer,
Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases.
2003,
Pubmed
Wlodawer,
Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes.
2001,
Pubmed
Wlodawer,
Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase.
2001,
Pubmed
