PDBsum entry 3ee6

Hydrolase

PDB id: 3ee6

Contents

Protein chain

529 a.a. *

Ligands

NAG ×8

SO4 ×2

Metals

_ZN ×8

_CL ×2

_CA ×2

Waters ×73

* Residue conservation analysis

PDB id:

3ee6

Name:

Hydrolase

Title:

Crystal structure analysis of tripeptidyl peptidase -i

Structure:

Tripeptidyl-peptidase 1. Chain: a, b. Synonym: tpp-1, tripeptidyl-peptidase i, tpp-i, tripeptidyl aminopeptidase, lysosomal pepstatin-insensitive protease, lpic, cell growth-inhibiting gene 1 protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cln2. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek 293.

Resolution:

2.35Å R-factor: 0.221 R-free: 0.262

Authors:

A.Pal,R.Kraetzner,M.Grapp,T.Gruene,K.Schreiber,M.Granborg,H.Urlaub, A.R.Asif,S.Becker,J.Gartner,G.M.Sheldrick,R.Steinfeld

Key ref:

A.Pal et al. (2009). Structure of tripeptidyl-peptidase I provides insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis. J Biol Chem, 284, 3976-3984. PubMed id: 19038966 DOI: 10.1074/jbc.M806947200

Date:

04-Sep-08 Release date: 25-Nov-08

Protein chains

O14773  (TPP1_HUMAN) -  Tripeptidyl-peptidase 1 from Homo sapiens

Seq: 563 a.a.

Struc: 529 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.14.9 - tripeptidyl-peptidase I.
• Reaction: Release of an N-terminal tripeptide from a polypeptide, but also endopeptidase activity.

DOI no: 10.1074/jbc.M806947200

J Biol Chem 284:3976-3984 (2009)

PubMed id: 19038966

Structure of tripeptidyl-peptidase I provides insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis.

A.Pal, R.Kraetzner, T.Gruene, M.Grapp, K.Schreiber, M.Grønborg, H.Urlaub, S.Becker, A.R.Asif, J.Gärtner, G.M.Sheldrick, R.Steinfeld.

ABSTRACT

Late infantile neuronal ceroid lipofuscinosis, a fatal neurodegenerative disease of childhood, is caused by mutations in the TPP1 gene that encodes tripeptidyl-peptidase I. We show that purified TPP1 requires at least partial glycosylation for in vitro autoprocessing and proteolytic activity. We crystallized the fully glycosylated TPP1 precursor under conditions that implied partial autocatalytic cleavage between the prosegment and the catalytic domain. X-ray crystallographic analysis at 2.35 angstroms resolution reveals a globular structure with a subtilisin-like fold, a Ser475-Glu272-Asp360 catalytic triad, and an octahedrally coordinated Ca2+-binding site that are characteristic features of the S53 sedolisin family of peptidases. In contrast to other S53 peptidases, the TPP1 structure revealed steric constraints on the P4 substrate pocket explaining its preferential cleavage of tripeptides from the unsubstituted N terminus of proteins. Two alternative conformations of the catalytic Asp276 are associated with the activation status of TPP1. 28 disease-causing missense mutations are analyzed in the light of the TPP1 structure providing insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis.

Selected figure(s)

Figure 4.
Topology diagram of the TPP1 structure showing the prosegment (Ser^20-Ser^180) and the catalytic domain (His^197-Pro^563).α-Helices are labeled α and are represented by cylinders, and β-strands are labeled β and represented by arrows. Residues that are involved in the catalytic mechanism are marked by red letters; the 6 cysteine residues that form disulfide bridges are colored yellow on black background, and the asparagine residues that carry N-linked oligosaccharides are highlighted by a turquoise background. No density could be observed for a possible glycosylation at Asn^222 (highlighted with gray background). The linker region (Ser^181-Leu^196) was poorly defined (gray letters). The first amino acid R of the purification tag RSHHHHHH is displayed in gray.

Figure 9.
Molecular basis of late infantile neuronal ceroid lipofuscinosis. A, view from the top of the cartoon model in Fig. 3D and rotated. The currently known pathogenic TPP1 missense mutations are mapped onto the TPP1 structure as labeled spheres and are colored according to their impact on the TPP1 structure. Red colored spheres point to mutations compromising the catalytic activity; blue colored spheres indicate conformational destabilization, and gray colored spheres designate unclear structural consequences. The Asn^286 residue (turquoise) corresponds to one of the five N-glycosylation sites. B, view of the catalytic cleft of the cartoon model in Fig. 3D. TPP1 missense mutations are shown as stick models, coloring scheme corresponds to A, except for mutations with unclear effect that are colored in green.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 3976-3984) copyright 2009.

Figures were selected by an automated process.