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PDBsum entry 2nsm

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protein ligands links
Hydrolase PDB id
2nsm
Jmol
Contents
Protein chain
390 a.a. *
Ligands
NAG ×3
SO4 ×4
Waters ×370
* Residue conservation analysis
PDB id:
2nsm
Name: Hydrolase
Title: Crystal structure of the human carboxypeptidase n (kininase catalytic domain
Structure: Carboxypeptidase n catalytic chain. Chain: a. Synonym: cpn, carboxypeptidase n polypeptide 1, carboxypept small subunit, lysine carboxypeptidase, arginine carboxypep kininase-1, serum carboxypeptidase n, scpn, anaphylatoxin inactivator, plasma carboxypeptidase b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Resolution:
2.10Å     R-factor:   0.179     R-free:   0.201
Authors: C.Keil,K.Maskos,M.Than,J.T.Hoopes,R.Huber,F.Tan,P.A.Deddish, E.G.Erdoes,R.A.Skidgel,W.Bode
Key ref:
C.Keil et al. (2007). Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain. J Mol Biol, 366, 504-516. PubMed id: 17157876 DOI: 10.1016/j.jmb.2006.11.025
Date:
05-Nov-06     Release date:   24-Apr-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15169  (CBPN_HUMAN) -  Carboxypeptidase N catalytic chain
Seq:
Struc:
458 a.a.
390 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.17.3  - Lysine carboxypeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidyl-L-lysine(or L-arginine) + H(2)O = peptide + L-lysine(or L- arginine)
135953188 ×
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     bradykinin catabolic process   3 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
DOI no: 10.1016/j.jmb.2006.11.025 J Mol Biol 366:504-516 (2007)
PubMed id: 17157876  
 
 
Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain.
C.Keil, K.Maskos, M.Than, J.T.Hoopes, R.Huber, F.Tan, P.A.Deddish, E.G.Erdös, R.A.Skidgel, W.Bode.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo representation of the human CPN1 ribbon, with the catalytic domain on top and the cylindrical TT domain at the bottom. Helices (α1 to α9) and β-strands (β1 to β15) are represented as golden helices and blue arrows, and the residual chain as a red rope. In addition are shown the catalytic zinc ion inserted according to the CPM structure (purple sphere), the two disulfide bridges (yellow stick model), the three glycosylated residues Thr380, Thr382 and Thr389, and the O-linked proximal sugars (orange as well as green stick models, respectively). The Figure was prepared with PyMol [http://pymol.sourceforge.net/]. Figure 1. Stereo representation of the human CPN1 ribbon, with the catalytic domain on top and the cylindrical TT domain at the bottom. Helices (α1 to α9) and β-strands (β1 to β15) are represented as golden helices and blue arrows, and the residual chain as a red rope. In addition are shown the catalytic zinc ion inserted according to the CPM structure (purple sphere), the two disulfide bridges (yellow stick model), the three glycosylated residues Thr380, Thr382 and Thr389, and the O-linked proximal sugars (orange as well as green stick models, respectively). The Figure was prepared with PyMol [http://pymol.sourceforge.net/].
Figure 5.
Figure 5. Stereo view of CPN1, represented by its Connolly surface. Surface coloring is according to the electrostatic surface potential, ranging from negative (red, − 10 ek^− 1T^− 1) to positive (blue, 10 ek^− 1T^− 1). The catalytic zinc ion (purple sphere) has been inserted to indicate the active-site groove. The three O-linked sugars are shown as green sticks. Some exposed hydrophobic residues forming a belt-like hydrophobic surface patch wrapping around the CP-TT interface (possibly representing the attachment site for the 83 kDa CPN2 subunit) are labeled. Figure 5. Stereo view of CPN1, represented by its Connolly surface. Surface coloring is according to the electrostatic surface potential, ranging from negative (red, − 10 ek^− 1T^− 1) to positive (blue, 10 ek^− 1T^− 1). The catalytic zinc ion (purple sphere) has been inserted to indicate the active-site groove. The three O-linked sugars are shown as green sticks. Some exposed hydrophobic residues forming a belt-like hydrophobic surface patch wrapping around the CP-TT interface (possibly representing the attachment site for the 83 kDa CPN2 subunit) are labeled. The Figure was prepared with GRASP.[3]^57
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 366, 504-516) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20065150 E.G.Erdös, F.Tan, and R.A.Skidgel (2010).
Angiotensin I-converting enzyme inhibitors are allosteric enhancers of kinin B1 and B2 receptor function.
  Hypertension, 55, 214-220.  
18566513 I.Pallarès, D.Fernández, M.Comellas-Bigler, J.Fernández-Recio, S.Ventura, F.X.Avilés, W.Bode, and J.Vendrell (2008).
Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid).
  Acta Crystallogr D Biol Crystallogr, 64, 784-791.
PDB code: 2v77
18187413 X.Zhang, F.Tan, Y.Zhang, and R.A.Skidgel (2008).
Carboxypeptidase M and kinin B1 receptors interact to facilitate efficient b1 signaling from B2 agonists.
  J Biol Chem, 283, 7994-8004.  
18039526 R.A.Skidgel, and E.G.Erdös (2007).
Structure and function of human plasma carboxypeptidase N, the anaphylatoxin inactivator.
  Int Immunopharmacol, 7, 1888-1899.  
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