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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.27.5
- Pancreatic ribonuclease.
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Reaction:
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Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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2 terms
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Biological process
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chemotaxis
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2 terms
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Biochemical function
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nucleic acid binding
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6 terms
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DOI no:
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Biochemistry
41:3341-3352
(2002)
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PubMed id:
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Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.
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G.J.Swaminathan,
D.E.Holloway,
K.Veluraja,
K.R.Acharya.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.Torrent,
M.V.Nogués,
and
E.Boix
(2011).
Eosinophil cationic protein (ECP) can bind heparin and other glycosaminoglycans through its RNase active site.
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J Mol Recognit, 24,
90.
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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.
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Biol Chem, 390,
225-234.
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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.
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Biochemistry, 48,
7160-7168.
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H.F.Rosenberg
(2008).
Eosinophil-derived neurotoxin / RNase 2: connecting the past, the present and the future.
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Curr Pharm Biotechnol, 9,
135-140.
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J.Arunachalam,
and
N.Gautham
(2008).
Hydrophobic clusters in protein structures.
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Proteins, 71,
2012-2025.
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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.
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J Mol Biol, 380,
206-222.
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PDB codes:
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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.
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Mol Cell Biochem, 303,
175-181.
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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.
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BMC Bioinformatics, 7,
38.
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N.Narayana
(2006).
High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site.
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Acta Crystallogr D Biol Crystallogr, 62,
695-706.
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PDB code:
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K.Kumar,
M.Brady,
and
R.Shapiro
(2004).
Selective abolition of pancreatic RNase binding to its inhibitor protein.
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Proc Natl Acad Sci U S A, 101,
53-58.
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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.
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Protein Sci, 12,
2559-2574.
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PDB codes:
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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.
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Biochemistry, 41,
12100-12106.
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PDB code:
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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.
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Links
