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PDBsum entry 1e21

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protein links
Hydrolase PDB id
1e21
Jmol
Contents
Protein chain
120 a.a. *
Waters ×137
* Residue conservation analysis
PDB id:
1e21
Name: Hydrolase
Title: Ribonuclease 1 des1-7 crystal structure at 1.9a
Structure: Ribonuclease 1. Chain: a. Synonym: rnase 1. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: pancreas. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.195     R-free:   0.251
Authors: J.Pous,G.Mallorqui-Fernandez,R.Peracaula,S.S.Terzyan, J.Futami,H.Tada,H.Yamada,M.Seno,R.De Llorens, F.X.Gomis-Ruth,M.Coll
Key ref:
J.Pous et al. (2001). Three-dimensional structure of human RNase 1 delta N7 at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr, 57, 498-505. PubMed id: 11264578 DOI: 10.1107/S0907444901001147
Date:
15-May-00     Release date:   03-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic
Seq:
Struc:
156 a.a.
120 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     6 terms  

 

 
DOI no: 10.1107/S0907444901001147 Acta Crystallogr D Biol Crystallogr 57:498-505 (2001)
PubMed id: 11264578  
 
 
Three-dimensional structure of human RNase 1 delta N7 at 1.9 A resolution.
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, M.Coll.
 
  ABSTRACT  
 
Human pancreatic ribonuclease 1 (RNase 1) is considered to be the human counterpart of bovine pancreatic RNase A. Truncation of seven amino-acid residues from the amino-terminal sequence resulted in RNase 1 Delta N7, which has a reduced ribonucleolytic activity and a lower affinity for the human placental RNase inhibitor (PRI). This RNase 1 variant has been cloned, heterologously overexpressed, purified and crystallized. Its crystal structure has been determined and refined using data to 1.9 A resolution. The molecule displays the alpha + beta folding topology typical of members of the RNase A superfamily. The main distinct features found in RNase 1 Delta N7 are basically located in three loops affecting the fitting of the enzyme to the active site of subtilisin and the shape of the B2 subsite. These changes, taken with the lack of the catalytically active residue Lys7, may explain the reduced affinity of RNase 1 Delta N7 for PRI and the low ribonucleolytic activity of the protein when compared with the native enzyme.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 (a) Ribbon representation of the RNase 1 N7 polypeptide fold. The labelled helices ( 1- 3), strands ( 1- 6) and loops are shown as helical ribbons, arrows and thin tubes, respectively. Labelling is according to Fig. 1-. (b) Superimposed RNase C^ structures. The displayed traces correspond to RNase 1 N7 (cyan blue), human ECP (blue; PDB code [231]1dyt ), EDN (green), RNase 4 (red; PDB code [232]1rnf ) and angiogenin (yellow; PDB code [233]1ang ). Some RNase 1 [234][Delta] N7 residues are labelled.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 498-505) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21235798 J.Bystrom, K.Amin, and D.Bishop-Bailey (2011).
Analysing the eosinophil cationic protein - a clue to the function of the eosinophil granulocyte.
  Respir Res, 12, 10.  
  19177350 A.Merlino, G.Avella, S.Di Gaetano, A.Arciello, R.Piccoli, L.Mazzarella, and F.Sica (2009).
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
  Protein Sci, 18, 50-57.
PDB code: 3f8g
17350650 R.J.Johnson, J.G.McCoy, C.A.Bingman, G.N.Phillips, and R.T.Raines (2007).
Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein.
  J Mol Biol, 368, 434-449.
PDB codes: 1z7x 2q4g
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.  
16335788 D.Gaur, and J.K.Batra (2005).
Role of aspartic acid 121 in human pancreatic ribonuclease catalysis.
  Mol Cell Biochem, 275, 95.  
12833549 F.Sica, A.Di Fiore, A.Zagari, and L.Mazzarella (2003).
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative.
  Proteins, 52, 263-271.
PDB codes: 1n1x 1n3z
12737851 M.V.Backer, T.I.Gaynutdinov, I.I.Gorshkova, R.J.Crouch, T.Hu, R.Aloise, M.Arab, K.Przekop, and J.M.Backer (2003).
Humanized docking system for assembly of targeting drug delivery complexes.
  J Control Release, 89, 499-511.  
11555655 P.A.Leland, K.E.Staniszewski, B.M.Kim, and R.T.Raines (2001).
Endowing human pancreatic ribonuclease with toxicity for cancer cells.
  J Biol Chem, 276, 43095-43102.  
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.