Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain

J Mol Biol. 2007 Feb 16;366(2):504-16. doi: 10.1016/j.jmb.2006.11.025. Epub 2006 Nov 11.

Abstract

Human carboxypeptidase N (CPN), a member of the CPN/E subfamily of "regulatory" metallo-carboxypeptidases, is an extracellular glycoprotein synthesized in the liver and secreted into the blood, where it controls the activity of vasoactive peptide hormones, growth factors and cytokines by specifically removing C-terminal basic residues. Normally, CPN circulates in blood plasma as a hetero-tetramer consisting of two 83 kDa (CPN2) domains each flanked by a 48 to 55 kDa catalytic (CPN1) domain. We have prepared and crystallized the recombinant C-terminally truncated catalytic domain of human CPN1, and have determined and refined its 2.1 A crystal structure. The structural analysis reveals that CPN1 has a pear-like shape, consisting of a 319 residue N-terminal catalytic domain and an abutting, cylindrically shaped 79 residue C-terminal beta-sandwich transthyretin (TT) domain, more resembling CPD-2 than CPM. Like these other CPN/E members, two surface loops surrounding the active-site groove restrict access to the catalytic center, offering an explanation for why some larger protein carboxypeptidase inhibitors do not inhibit CPN. Modeling of the Pro-Phe-Arg C-terminal end of the natural substrate bradykinin into the active site shows that the S1' pocket of CPN1 might better accommodate P1'-Lys than Arg residues, in agreement with CPN's preference for cleaving off C-terminal Lys residues. Three Thr residues at the distal TT edge of CPN1 are O-linked to N-acetyl glucosamine sugars; equivalent sites in the membrane-anchored CPM are occupied by basic residues probably involved in membrane interaction. In tetrameric CPN, each CPN1 subunit might interact with the central leucine-rich repeat tandem of the cognate CPN2 subunit via a unique hydrophobic surface patch wrapping around the catalytic domain-TT interface, exposing the two active centers.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Bradykinin / chemistry
  • Catalytic Domain*
  • Crystallography, X-Ray
  • Humans
  • Lysine Carboxypeptidase / chemistry*
  • Lysine Carboxypeptidase / genetics
  • Lysine Carboxypeptidase / isolation & purification
  • Models, Molecular
  • Molecular Sequence Data
  • Prealbumin / chemistry
  • Protein Structure, Tertiary*
  • Sequence Analysis, Protein
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship

Substances

  • Prealbumin
  • Lysine Carboxypeptidase
  • Bradykinin

Associated data

  • PDB/2NSM