1BY8 | pdb_00001by8
THE CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN K
- PDB DOI: https://doi.org/10.2210/pdb1BY8/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 1998-10-27 Released: 1999-10-24
- Deposition Author(s): Lalonde, J.M., Zhao, B., Smith, W.W., Janson, C.A., Desjarlais, R.L., Tomaszek, T.A., Carr, T.J., Thompson, S.K., Yamashita, D.S., Veber, D.F., Abdel-Mequid, S.S.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.344 (Depositor)
- R-Value Work: 0.214 (Depositor)
- R-Value Observed: 0.214 (Depositor)
Starting Model: experimental
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Literature
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The crystal structure of human procathepsin K.
LaLonde, J.M., Zhao, B., Janson, C.A., D'Alessio, K.J., McQueney, M.S., Orsini, M.J., Debouck, C.M., Smith, W.W.(1999) Biochemistry 38: 862-869
- PubMed: 9893980 Search on PubMed
- DOI: https://doi.org/10.1021/bi9822271
- Primary Citation Related Structures:
1BY8 - PubMed Abstract:
Cathepsin K is a cysteine protease present in human osteoclasts that plays an important role in bone resorption. Cathepsin K is synthesized as an inactive proenzyme and activated under conditions of low pH. Autoproteolytic processing of the N-terminal 99 amino acid propeptide produces the active, mature form of cathepsin K. It is presumed that the activation of procathepsin K in vivo occurs in the bone resorption pit, which has a low-pH environment. We have determined the structure of human procathepsin K at 2.8 A resolution. The structure of the mature enzyme domain within procathepsin K is virtually identical to that of mature cathepsin K. The fold of the propeptide of procathepsin K is similar to that observed in procathepsins B and L despite differences in length and sequence. A portion of the propeptide occupies the active site cleft of cathepsin K. Hydrophobic interactions, salt bridges, and hydrogen-bonding interactions are observed in the structure of the propeptide and between the propeptide and the mature enzyme of procathepsin K. These interactions suggest an explanation for the stability of the proenzyme. The structure of procathepsin K contributes to an understanding of the molecular basis of inhibition by the propeptide portion of the molecule and activation of this important member of the cysteine protease family.
- Department of Structural Biology, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA.
Organizational Affiliation:
Biological Assembly 1
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Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 35.36 kDa
- Atom Count: 2,447
- Modeled Residue Count: 310
- Deposited Residue Count: 314
- Unique protein chains: 1
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PROTEIN (PROCATHEPSIN K) | 314 | Homo sapiens | Mutation(s): 0 EC: 3.4.22.38 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P43235 GTEx: ENSG00000143387 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P43235 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.344 (Depositor)
- R-Value Work: 0.214 (Depositor)
- R-Value Observed: 0.214 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.78 | α = 90 |
| b = 156.55 | β = 90 |
| c = 96.26 | γ = 90 |
| Software Name | Purpose |
|---|---|
| X-GEN | data scaling |
| X-GEN | data reduction |
| X-PLOR | model building |
| X-PLOR | refinement |
| X-PLOR | phasing |
Entry History
Deposition Data
- Released Date: 1999-10-24 Deposition Author(s): Lalonde, J.M., Zhao, B., Smith, W.W., Janson, C.A., Desjarlais, R.L., Tomaszek, T.A., Carr, T.J., Thompson, S.K., Yamashita, D.S., Veber, D.F., Abdel-Mequid, S.S.
Revision History (Full details and data files)
- Version 1.0: 1999-10-24
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2017-10-04
Changes: Refinement description - Version 1.4: 2023-08-09
Changes: Data collection, Database references, Refinement description - Version 1.5: 2024-11-13
Changes: Structure summary
