5MRV

Crystal structure of human carboxypeptidase O in complex with NvCI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure and mechanism of human carboxypeptidase O: Insights into its specific activity for acidic residues.

Garcia-Guerrero, M.C.Garcia-Pardo, J.Berenguer, E.Fernandez-Alvarez, R.Barfi, G.B.Lyons, P.J.Aviles, F.X.Huber, R.Lorenzo, J.Reverter, D.

(2018) Proc Natl Acad Sci U S A 115: E3932-E3939

  • DOI: https://doi.org/10.1073/pnas.1803685115
  • Primary Citation of Related Structures:  
    5MRV

  • PubMed Abstract: 

    Human metallocarboxypeptidase O (hCPO) is a recently discovered digestive enzyme localized to the apical membrane of intestinal epithelial cells. Unlike pancreatic metallocarboxypeptidases, hCPO is glycosylated and produced as an active enzyme with distinctive substrate specificity toward C-terminal (C-t) acidic residues. Here we present the crystal structure of hCPO at 1.85-Å resolution, both alone and in complex with a carboxypeptidase inhibitor (NvCI) from the marine snail Nerita versicolor The structure provides detailed information regarding determinants of enzyme specificity, in particular Arg275, placed at the bottom of the substrate-binding pocket. This residue, located at "canonical" position 255, where it is Ile in human pancreatic carboxypeptidases A1 (hCPA1) and A2 (hCPA2) and Asp in B (hCPB), plays a dominant role in determining the preference of hCPO for acidic C-t residues. Site-directed mutagenesis to Asp and Ala changes the specificity to C-t basic and hydrophobic residues, respectively. The single-site mutants thus faithfully mimic the enzymatic properties of CPB and CPA, respectively. hCPO also shows a preference for Glu over Asp, probably as a consequence of a tighter fitting of the Glu side chain in its S1' substrate-binding pocket. This unique preference of hCPO, together with hCPA1, hCPA2, and hCPB, completes the array of C-t cleavages enabling the digestion of the dietary proteins within the intestine. Finally, in addition to activity toward small synthetic substrates and peptides, hCPO can also trim C-t extensions of proteins, such as epidermal growth factor, suggesting a role in the maturation and degradation of growth factors and bioactive peptides.


  • Organizational Affiliation

    Institute for Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase O
A, B
355Homo sapiensMutation(s): 2 
Gene Names: CPO
EC: 3.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVL8 (Homo sapiens)
Explore Q8IVL8 
Go to UniProtKB:  Q8IVL8
PHAROS:  Q8IVL8
GTEx:  ENSG00000144410 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVL8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Metallocarboxypeptidase inhibitor53Nerita versicolorMutation(s): 0 
UniProt
Find proteins for P86912 (Nerita versicolor)
Explore P86912 
Go to UniProtKB:  P86912
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP86912
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.114α = 90
b = 72.144β = 94.66
c = 90.187γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary