2ZCH

Crystal structure of human prostate specific antigen complexed with an activating antibody

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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This is version 2.0 of the entry. See complete history. 


Literature

Crystal structure of a ternary complex between human prostate-specific antigen, its substrate acyl intermediate and an activating antibody

Michel, S., Muller, B.H., Bossus, M., Ducancel, F., Jolivet-Reynaud, C., Stura, E.A.

(2008) J Mol Biol 376: 1021-1033

  • DOI: 10.1016/j.jmb.2007.11.052
  • Primary Citation of Related Structures:  
    2ZCK, 2ZCL, 2ZCH

  • PubMed Abstract: 

    • Human prostate-specific antigen (PSA or KLK3) is an important marker for the diagnosis and management of prostate cancer. This is an androgen-regulated glycoprotein of the kallikrein-related protease family secreted by prostatic epithelial cells. Its physiological function is to cleave semenogelins in the seminal coagulum and its enzymatic activity is strongly modulated by zinc ions ...

    Human prostate-specific antigen (PSA or KLK3) is an important marker for the diagnosis and management of prostate cancer. This is an androgen-regulated glycoprotein of the kallikrein-related protease family secreted by prostatic epithelial cells. Its physiological function is to cleave semenogelins in the seminal coagulum and its enzymatic activity is strongly modulated by zinc ions. Here we present the first crystal structure of human PSA in complex with monoclonal antibody (mAb) 8G8F5 that enhances its enzymatic activity. The mAb recognizes an epitope composed of five discontinuous segments including residues from the kallikrein loop and stabilizes PSA in an "open and active conformation" that accelerates catalysis. We also present the crystal structure of PSA in complex with both the mAb 8G8F5 and a fluorogenic substrate Mu-KGISSQY-AFC, derived from semenogelin I. By exploiting the inhibition of PSA by zinc ions, we were able to obtain a substrate acyl intermediate covalently linked to the catalytic serine, at pH 7.3 but not at pH 5.5. Moreover, the inhibition of PSA activity by zinc was found to be modulated by pH variations but not by the antibody binding. The correlation of the different data with the physiological conditions under which PSA can cleave semenogelins is discussed.

    Organizational Affiliation: 

    CEA, iBiTec-S/SIMOPRO, LTMB, Gif-sur-Yvette, F-91191, France.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostate-specific antigen P237Homo sapiensMutation(s): 0 
Gene Names: KLK3, APS
EC: 3.4.21.77
Find proteins for P07288 (Homo sapiens)
Explore P07288 
Go to UniProtKB:  P07288
NIH Common Fund Data Resources
PHAROS:  P07288
GTEx:  ENSG00000142515
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
monoclonal antibody 8G8F5 Fab L215Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
monoclonal antibody 8G8F5 Fab H229Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG
Download Ideal Coordinates CCD File 
P
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
P
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.36α = 90
b = 87.36β = 90
c = 236.332γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOSFLMdata reduction
PROCESSdata scaling
XFITdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary