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PDBsum entry 1gqv

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Rnase-2 PDB id
1gqv
Jmol
Contents
Protein chain
135 a.a. *
Ligands
ACT
Waters ×226
* Residue conservation analysis
PDB id:
1gqv
Name: Rnase-2
Title: Atomic resolution (0.98a) structure of eosinophil-derived neurotoxin
Structure: Eosinophil-derived neurotoxin. Chain: a. Synonym: rnase-2, rnase-us, edn. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Cell: eosinophil. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
0.98Å     R-factor:   0.115     R-free:   0.144
Authors: G.J.Swaminathan,D.E.Holloway,K.Veluraja,K.R.Acharya
Key ref:
G.J.Swaminathan et al. (2002). Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin. Biochemistry, 41, 3341-3352. PubMed id: 11876642 DOI: 10.1021/bi015911f
Date:
05-Dec-01     Release date:   08-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10153  (RNAS2_HUMAN) -  Non-secretory ribonuclease
Seq:
Struc:
161 a.a.
135 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   5 terms 
  Biochemical function     nucleic acid binding     6 terms  

 

 
DOI no: 10.1021/bi015911f Biochemistry 41:3341-3352 (2002)
PubMed id: 11876642  
 
 
Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.
G.J.Swaminathan, D.E.Holloway, K.Veluraja, K.R.Acharya.
 
  ABSTRACT  
 
Human eosinophil-derived neurotoxin (EDN) is a small, basic protein that belongs to the ribonuclease A superfamily. EDN displays antiviral activity and causes the neurotoxic Gordon phenomenon when injected into rabbits. Although EDN and ribonuclease A have appreciable structural similarity and a conserved catalytic triad, their peripheral substrate-binding sites are not conserved. The crystal structure of recombinant EDN (rEDN) has been determined at 0.98 A resolution from data collected at a low temperature (100 K). We have refined the crystallographic model of the structure using anisotropic displacement parameters to a conventional R-factor of 0.116. This represents the highest resolution structure of rEDN determined to date and is only the second ribonuclease structure to be determined at a resolution greater than 1.0 A. The structure provides a detailed picture of the conformational freedom at the various subsites of rEDN, and the water structure accounts for more than 50% of the total solvent content of the unit cell. This information will be crucial for the design of tight-binding inhibitors to restrain the ribonucleolytic activity of rEDN.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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.  
18673278 H.F.Rosenberg (2008).
Eosinophil-derived neurotoxin / RNase 2: connecting the past, the present and the future.
  Curr Pharm Biotechnol, 9, 135-140.  
18186486 J.Arunachalam, and N.Gautham (2008).
Hydrophobic clusters in protein structures.
  Proteins, 71, 2012-2025.  
18508078 K.Kazakou, D.E.Holloway, S.H.Prior, V.Subramanian, and K.R.Acharya (2008).
Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications.
  J Mol Biol, 380, 206-222.
PDB codes: 2vq8 2vq9
17483910 D.Sikriwal, D.Seth, P.Dey, and J.K.Batra (2007).
Human eosinophil-derived neurotoxin: involvement of a putative non-catalytic phosphate-binding subsite in its catalysis.
  Mol Cell Biochem, 303, 175-181.  
16433931 H.T.Chang, T.W.Pai, T.C.Fan, B.H.Su, P.C.Wu, C.Y.Tang, C.T.Chang, S.H.Liu, and M.D.Chang (2006).
A reinforced merging methodology for mapping unique peptide motifs in members of protein families.
  BMC Bioinformatics, 7, 38.  
16790925 N.Narayana (2006).
High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site.
  Acta Crystallogr D Biol Crystallogr, 62, 695-706.
PDB code: 2gqv
14681553 K.Kumar, M.Brady, and R.Shapiro (2004).
Selective abolition of pancreatic RNase binding to its inhibitor protein.
  Proc Natl Acad Sci U S A, 101, 53-58.  
14573867 D.D.Leonidas, G.B.Chavali, N.G.Oikonomakos, E.D.Chrysina, M.N.Kosmopoulou, M.Vlassi, C.Frankling, and K.R.Acharya (2003).
High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.
  Protein Sci, 12, 2559-2574.
PDB codes: 1o0f 1o0h 1o0m 1o0n 1o0o
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
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 codes are shown on the right.