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PDBsum entry 1dyt
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1dyt

 

 

 

 

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Contents
Protein chain
133 a.a. *
Ligands
CIT ×4
Metals
_FE ×2
Waters ×332
* Residue conservation analysis
PDB id:
1dyt
Name: Hydrolase
Title: X-ray crystal structure of ecp (rnase 3) at 1.75 a
Structure: Eosinophil cationic protein. Chain: a, b. Synonym: ribonuclease 3. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell: eosinophil. Gene: rnase3. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.75Å     R-factor:   0.224     R-free:   0.271
Authors: G.Mallorqui-Fernandez,J.Pous,R.Peracaula,T.Maeda,H.Tada,H.Yamada, M.Seno,R.De Llorens,F.X.Gomis-Rueth,M.Coll
Key ref:
G.Mallorquí-Fernández et al. (2000). Three-dimensional crystal structure of human eosinophil cationic protein (RNase 3) at 1.75 A resolution. J Mol Biol, 300, 1297-1307. PubMed id: 10903870 DOI: 10.1006/jmbi.2000.3939
Date:
08-Feb-00     Release date:   08-Feb-01    
PROCHECK
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 Headers
 References

Protein chains
P12724  (ECP_HUMAN) -  Eosinophil cationic protein from Homo sapiens
Seq:
Struc: 		160 a.a.
133 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1006/jmbi.2000.3939 J Mol Biol 300:1297-1307 (2000)
PubMed id: 10903870  
 
 
Three-dimensional crystal structure of human eosinophil cationic protein (RNase 3) at 1.75 A resolution.
G.Mallorquí-Fernández, J.Pous, R.Peracaula, J.Aymamí, T.Maeda, H.Tada, H.Yamada, M.Seno, R.de Llorens, F.X.Gomis-Rüth, M.Coll.
 
  ABSTRACT  
 
Eosinophil cationic protein (ECP; RNase 3) is a human ribonuclease found only in eosinophil leukocytes that belongs to the RNase A superfamily. This enzyme is bactericidal, helminthotoxic and cytotoxic to mammalian cells and tissues. The protein has been cloned, heterologously overexpressed, purified and crystallized. Its crystal structure has been determined and refined using data up to 1. 75 A resolution. The molecule displays the alpha+beta folding topology typical for members of the ribonuclease A superfamily. The catalytic active site residues are conserved with respect to other ribonucleases of the superfamily but some differences appear at substrate recognition subsites, which may account, in part, for the low catalytic activity. Most strikingly, 19 surface-located arginine residues confer a strong basic character to the protein. The high concentration of positive charges and the particular orientation of the side-chains of these residues may also be related to the low activity of ECP as a ribonuclease and provides an explanation for its unique cytotoxic role through cell membrane disruption.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Ribbon representation of the ECP polypep- tide fold. The labelled helices (a1-a3), strands (b1-b6) and loops are shown as helical ribbons, arrows and thin tubes, respectively. Labelling is according to Figure 1. 		Figure 3.
Figure 3. View of the Connolly surfaces displaying the electrostatic potential (ranging from -15 kBT/e (red) to +15 kBT/e (blue)) of ECP (top), view into (a) and along (b) the active site cleft, and RNase A (bottom), view into (c) and along (d) the active site cleft.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 1297-1307) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21303303 A.Singh, and J.K.Batra (2011).
Role of unique basic residues in cytotoxic, antibacterial and antiparasitic activities of human eosinophil cationic protein.
  Biol Chem, 392, 337-346.  
20213669 M.Torrent, M.V.Nogués, and E.Boix (2011).
Eosinophil cationic protein (ECP) can bind heparin and other glycosaminoglycans through its RNase active site.
  J Mol Recognit, 24, 90.  
20180804 M.Torrent, M.Badia, M.Moussaoui, D.Sanchez, M.V.Nogués, and E.Boix (2010).
Comparison of human RNase 3 and RNase 7 bactericidal action at the Gram-negative and Gram-positive bacterial cell wall.
  FEBS J, 277, 1713-1725.  
20522258 Z.Wang, S.Kim, S.K.Quinney, J.Zhou, and L.Li (2010).
Non-compartment model to compartment model pharmacokinetics transformation meta-analysis--a multivariate nonlinear mixed model.
  BMC Syst Biol, 4, S8.  
19090717 D.Sikriwal, D.Seth, and J.K.Batra (2009).
Role of catalytic and non-catalytic subsite residues in ribonuclease activity of human eosinophil-derived neurotoxin.
  Biol Chem, 390, 225-234.  
19189375 D.V.Laurents, M.Bruix, M.A.Jiménez, J.Santoro, E.Boix, M.Moussaoui, M.V.Nogués, and M.Rico (2009).
The (1)H, (13)C, (15)N resonance assignment, solution structure, and residue level stability of eosinophil cationic protein/RNase 3 determined by NMR spectroscopy.
  Biopolymers, 91, 1018-1028.
PDB code: 2kb5
19588901 N.Doucet, E.D.Watt, and J.P.Loria (2009).
The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.
  Biochemistry, 48, 7160-7168.  
18593710 T.C.Fan, S.L.Fang, C.S.Hwang, C.Y.Hsu, X.A.Lu, S.C.Hung, S.C.Lin, and M.D.Chang (2008).
Characterization of molecular interactions between eosinophil cationic protein and heparin.
  J Biol Chem, 283, 25468-25474.  
17460791 E.Boix, and M.V.Nogués (2007).
Mammalian antimicrobial proteins and peptides: overview on the RNase A superfamily members involved in innate host defence.
  Mol Biosyst, 3, 317-335.  
17586772 H.Yamada, T.Tamada, M.Kosaka, K.Miyata, S.Fujiki, M.Tano, M.Moriya, M.Yamanishi, E.Honjo, H.Tada, T.Ino, H.Yamaguchi, J.Futami, M.Seno, T.Nomoto, T.Hirata, M.Yoshimura, and R.Kuroki (2007).
'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines.
  Protein Sci, 16, 1389-1397.
PDB codes: 2e0j 2e0l 2e0m 2e0o
12356310 C.G.Mohan, E.Boix, H.R.Evans, Z.Nikolovski, M.V.Nogués, C.M.Cuchillo, and K.R.Acharya (2002).
The crystal structure of eosinophil cationic protein in complex with 2',5'-ADP at 2.0 A resolution reveals the details of the ribonucleolytic active site.
  Biochemistry, 41, 12100-12106.
PDB code: 1h1h
11784325 T.Maeda, M.Kitazoe, H.Tada, R.de Llorens, D.S.Salomon, M.Ueda, H.Yamada, and M.Seno (2002).
Growth inhibition of mammalian cells by eosinophil cationic protein.
  Eur J Biochem, 269, 307-316.  
11264578 J.Pous, G.Mallorquí-Fernández, R.Peracaula, S.S.Terzyan, J.Futami, H.Tada, H.Yamada, M.Seno, R.de Llorens, F.X.Gomis-Rüth, and M.Coll (2001).
Three-dimensional structure of human RNase 1 delta N7 at 1.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 498-505.
PDB code: 1e21
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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