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PDBsum entry 1z7x

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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1z7x
Jmol
Contents
Protein chains
126 a.a. *
460 a.a. *
Ligands
CIT
Waters ×854
* Residue conservation analysis
PDB id:
1z7x
Name: Hydrolase/hydrolase inhibitor
Title: X-ray structure of human ribonuclease inhibitor complexed with ribonuclease i
Structure: Ribonuclease i. Chain: x, z. Synonym: rnase 1, rnase a, rnase upi-1, rib-1, hp-rnase. Engineered: yes. Ribonuclease inhibitor. Chain: w, y. Synonym: ribonuclease/angiogenin inhibitor, rai, rnase inhibitor, ri. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rnase1, rib1, rns1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rnh, pri.
Biol. unit: Dimer (from PQS)
Resolution:
1.95Å     R-factor:   0.178     R-free:   0.236
Authors: J.G.Mccoy,R.J.Johnson,R.T.Raines,E.Bitto,C.A.Bingman, G.E.Wesenberg,S.T.M.Allard,G.N.Phillips Jr.,Center For Eukaryotic Structural Genomics (Cesg)
Key ref:
R.J.Johnson et al. (2007). Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein. J Mol Biol, 368, 434-449. PubMed id: 17350650 DOI: 10.1016/j.jmb.2007.02.005
Date:
28-Mar-05     Release date:   21-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic
Seq:
Struc:
156 a.a.
126 a.a.
Protein chains
Pfam   ArchSchema ?
P13489  (RINI_HUMAN) -  Ribonuclease inhibitor
Seq:
Struc:
461 a.a.
460 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     metabolic process   6 terms 
  Biochemical function     protein binding     7 terms  

 

 
DOI no: 10.1016/j.jmb.2007.02.005 J Mol Biol 368:434-449 (2007)
PubMed id: 17350650  
 
 
Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein.
R.J.Johnson, J.G.McCoy, C.A.Bingman, G.N.Phillips, R.T.Raines.
 
  ABSTRACT  
 
The ribonuclease inhibitor protein (RI) binds to members of the bovine pancreatic ribonuclease (RNase A) superfamily with an affinity in the femtomolar range. Here, we report on structural and energetic aspects of the interaction between human RI (hRI) and human pancreatic ribonuclease (RNase 1). The structure of the crystalline hRI x RNase 1 complex was determined at a resolution of 1.95 A, revealing the formation of 19 intermolecular hydrogen bonds involving 13 residues of RNase 1. In contrast, only nine such hydrogen bonds are apparent in the structure of the complex between porcine RI and RNase A. hRI, which is anionic, also appears to use its horseshoe-shaped structure to engender long-range Coulombic interactions with RNase 1, which is cationic. In accordance with the structural data, the hRI.RNase 1 complex was found to be extremely stable (t(1/2)=81 days; K(d)=2.9 x 10(-16) M). Site-directed mutagenesis experiments enabled the identification of two cationic residues in RNase 1, Arg39 and Arg91, that are especially important for both the formation and stability of the complex, and are thus termed "electrostatic targeting residues". Disturbing the electrostatic attraction between hRI and RNase 1 yielded a variant of RNase 1 that maintained ribonucleolytic activity and conformational stability but had a 2.8 x 10(3)-fold lower association rate for complex formation and 5.9 x 10(9)-fold lower affinity for hRI. This variant of RNase 1, which exhibits the largest decrease in RI affinity of any engineered ribonuclease, is also toxic to human erythroleukemia cells. Together, these results provide new insight into an unusual and important protein-protein interaction, and could expedite the development of human ribonucleases as chemotherapeutic agents.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the crystalline complex of hRI (green) and RNase 1 (blue). Ribbon diagram of the contents of the asymmetric unit in which the N-terminal β-strands of hRI from two molecular complexes form an antiparallel β-sheet. The image was created with the program PyMOL (DeLano Scientific, South San Francisco, CA). Figure 1. Structure of the crystalline complex of hRI (green) and RNase 1 (blue). Ribbon diagram of the contents of the asymmetric unit in which the N-terminal β-strands of hRI from two molecular complexes form an antiparallel β-sheet. The image was created with the program PyMOL (DeLano Scientific, South San Francisco, CA).
Figure 4.
Figure 4. Electron density at 1σ (2F[obs]–F[calc]) of key contact residues between hRI (green) and RNase 1 (purple). Specific residues shown in detail are (a) Arg39, (b) Asn67, and (c) Arg91. Highlighted regions are shown in wall-eyed stereo; interprotein hydrogen bonds are displayed by black dotted lines. Images were created with the program PyMOL. Figure 4. Electron density at 1σ (2F[obs]–F[calc]) of key contact residues between hRI (green) and RNase 1 (purple). Specific residues shown in detail are (a) Arg39, (b) Asn67, and (c) Arg91. Highlighted regions are shown in wall-eyed stereo; interprotein hydrogen bonds are displayed by black dotted lines. Images were created with the program PyMOL.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 368, 434-449) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322759 C.Andrady, S.K.Sharma, and K.A.Chester (2011).
Antibody-enzyme fusion proteins for cancer therapy.
  Immunotherapy, 3, 193-211.  
21144746 G.A.Ellis, M.L.Hornung, and R.T.Raines (2011).
Potentiation of ribonuclease cytotoxicity by a poly(amidoamine) dendrimer.
  Bioorg Med Chem Lett, 21, 2756-2758.  
21134128 U.Arnold, F.Leich, P.Neumann, H.Lilie, and R.Ulbrich-Hofmann (2011).
Crystal structure of RNase A tandem enzymes and their interaction with the cytosolic ribonuclease inhibitor.
  FEBS J, 278, 331-340.
PDB codes: 3mwq 3mwr 3mx8
20525292 C.Kim, J.Basner, and B.Lee (2010).
Detecting internally symmetric protein structures.
  BMC Bioinformatics, 11, 303.  
20691138 H.X.Zhou (2010).
Rate theories for biologists.
  Q Rev Biophys, 43, 219-293.  
  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
19641608 B.Köten, M.Simanski, R.Gläser, R.Podschun, J.M.Schröder, and J.Harder (2009).
RNase 7 contributes to the cutaneous defense against Enterococcus faecium.
  PLoS One, 4, e6424.  
19196002 G.Schreiber, G.Haran, and H.X.Zhou (2009).
Fundamental aspects of protein-protein association kinetics.
  Chem Rev, 109, 839-860.  
19402708 K.A.Dickson, and R.T.Raines (2009).
Silencing an inhibitor unleashes a cytotoxic enzyme.
  Biochemistry, 48, 5051-5053.  
19452560 K.L.Hindle, J.Bella, and S.C.Lovell (2009).
Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.
  Proteins, 77, 342-358.  
19523116 R.F.Turcotte, L.D.Lavis, and R.T.Raines (2009).
Onconase cytotoxicity relies on the distribution of its positive charge.
  FEBS J, 276, 3846-3857.  
18560598 E.Edelweiss, T.G.Balandin, J.L.Ivanova, G.V.Lutsenko, O.G.Leonova, V.I.Popenko, A.M.Sapozhnikov, and S.M.Deyev (2008).
Barnase as a new therapeutic agent triggering apoptosis in human cancer cells.
  PLoS ONE, 3, e2434.  
18979636 G.Torrent, A.Benito, J.Castro, M.Ribó, and M.Vilanova (2008).
Contribution of the C30/C75 disulfide bond to the biological properties of onconase.
  Biol Chem, 389, 1127-1136.  
18001769 J.E.Lee, E.Bae, C.A.Bingman, G.N.Phillips, and R.T.Raines (2008).
Structural basis for catalysis by onconase.
  J Mol Biol, 375, 165-177.
PDB codes: 2gmk 2i5s
18215091 J.E.Lee, and R.T.Raines (2008).
Ribonucleases as novel chemotherapeutics : the ranpirnase example.
  BioDrugs, 22, 53-58.  
18930025 R.F.Turcotte, and R.T.Raines (2008).
Interaction of onconase with the human ribonuclease inhibitor protein.
  Biochem Biophys Res Commun, 377, 512-514.  
18560425 R.H.Newman, and J.Zhang (2008).
Small molecules and chemical tools at the interface.
  Nat Chem Biol, 4, 382-386.  
18673284 T.J.Rutkoski, and R.T.Raines (2008).
Evasion of ribonuclease inhibitor as a determinant of ribonuclease cytotoxicity.
  Curr Pharm Biotechnol, 9, 185-189.  
18084271 U.S.Eggert, and G.Superti-Furga (2008).
Drugs in action.
  Nat Chem Biol, 4, 7.  
18673287 W.Ardelt, K.Shogen, and Z.Darzynkiewicz (2008).
Onconase and amphinase, the antitumor ribonucleases from Rana pipiens oocytes.
  Curr Pharm Biotechnol, 9, 215-225.  
17786587 G.N.Phillips, B.G.Fox, J.L.Markley, B.F.Volkman, E.Bae, E.Bitto, C.A.Bingman, R.O.Frederick, J.G.McCoy, B.L.Lytle, B.S.Pierce, J.Song, and S.N.Twigger (2007).
Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics.
  J Struct Funct Genomics, 8, 73-84.  
17956129 R.J.Johnson, L.D.Lavis, and R.T.Raines (2007).
Intraspecies regulation of ribonucleolytic activity.
  Biochemistry, 46, 13131-13140.  
17705507 R.J.Johnson, T.Y.Chao, L.D.Lavis, and R.T.Raines (2007).
Cytotoxic ribonucleases: the dichotomy of Coulombic forces.
  Biochemistry, 46, 10308-10316.  
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.