3EE6 | pdb_00003ee6

Crystal Structure Analysis of Tripeptidyl peptidase -I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.262 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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

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

(2009) J Biological Chem 284: 3976-3984

  • DOI: https://doi.org/10.1074/jbc.M806947200
  • Primary Citation Related Structures: 
    3EE6

  • PubMed 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.


  • Organizational Affiliation
    • Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, 34077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 127.39 kDa 
  • Atom Count: 8,361 
  • Modeled Residue Count: 1,058 
  • Deposited Residue Count: 1,142 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tripeptidyl-peptidase 1
A, B
571Homo sapiensMutation(s): 0 
Gene Names: CLN2
EC: 3.4.14.9
UniProt & NIH Common Fund Data Resources
Find proteins for O14773 (Homo sapiens)
Explore O14773 
Go to UniProtKB:  O14773
PHAROS:  O14773
GTEx:  ENSG00000166340 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14773
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
N [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
M [auth A],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
R [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
L [auth A],
W [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.262 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.45α = 90
b = 128.93β = 90
c = 100.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
SADABSdata scaling
SHELXDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-06-20
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary