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PDBsum entry 1rnu

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Hydrolase(phosphoric diester,RNA) PDB id
1rnu
Jmol
Contents
Protein chain
116 a.a. *
Ligands
SO4
Waters ×88
* Residue conservation analysis
PDB id:
1rnu
Name: Hydrolase(phosphoric diester,RNA)
Title: Refinement of the crystal structure of ribonuclease s. Comparison with and between the various ribonuclease a structures
Structure: Ribonuclease s. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.176    
Authors: E.E.Kim,R.Varadarajan,H.W.Wyckoff,F.M.Richards
Key ref:
E.E.Kim et al. (1992). Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures. Biochemistry, 31, 12304-12314. PubMed id: 1463719 DOI: 10.1021/bi00164a004
Date:
19-Feb-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
116 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1021/bi00164a004 Biochemistry 31:12304-12314 (1992)
PubMed id: 1463719  
 
 
Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures.
E.E.Kim, R.Varadarajan, H.W.Wyckoff, F.M.Richards.
 
  ABSTRACT  
 
Ribonuclease S (RNase-S) is a complex that consists of two proteolytic fragments of bovine pancreatic ribonuclease A (RNase-A): the S-peptide (residues 1-20) and S-protein (residues 21-124). We have refined the crystal structures of three RNase-S complexes. The first two contain the full-length 20-residue S-peptide and were studied at pHs of 4.75 and 5.5. The third one consists of a truncated form of S-peptide (residues 1-15) and was studied at pH 4.75 as the reference structure for a series of mutant peptide complexes to be reported separately. Excluding residues 16-23 which are either missing (in the S15 complex) or disordered (in both S20 complexes), all three structures refined at 1.6-A resolution are identical within the estimated errors in the coordinates (0.048 A for the backbone atoms). The R-values, residual error, range from 17.4% to 18.6%. The final model of S20, pH 4.75, includes 1 sulfate and 84 water molecules. The side chains of 11 residues were modeled in two discrete conformations. The final structures were independent of the particular RNase-A or RNase-S used as a starting model. An extensive comparison with refined crystal structures of RNase-A reveals that the core of the molecule which is held together with extensive hydrogen bonds is in identical pattern in all cases. However, the loop regions vary from one structure to another and are often characterized by high B-factors. The pattern of thermal parameters appears to be dependent on crystal packing and correlates well with the accessibility calculated in the crystal. Gln60 is a conserved residue in all sequences known to date for this class of ribonucleases. However, it is the only residue that is clearly defined in an unfavorable position (phi = -100 degrees, psi = -130 degrees) on the Ramachandran plot. The origin of the substantial differences between RNase-A and RNase-S in stability to both acid and temperature denaturation and in susceptibility to proteolysis at neutral pH is not obvious in our visual comparison of these two structures.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21325613 A.Bachmann, D.Wildemann, F.Praetorius, G.Fischer, and T.Kiefhaber (2011).
Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction.
  Proc Natl Acad Sci U S A, 108, 3952-3957.  
19490118 S.T.Philominathan, O.Matsushita, R.Gensure, and J.Sakon (2009).
Ca2+-induced linker transformation leads to a compact and rigid collagen-binding domain of Clostridium histolyticum collagenase.
  FEBS J, 276, 3589-3601.  
16415350 J.P.López-Alonso, M.Bruix, J.Font, M.Ribó, M.Vilanova, M.Rico, G.Gotte, M.Libonati, C.González, and D.V.Laurents (2006).
Formation, structure, and dissociation of the ribonuclease S three-dimensional domain-swapped dimer.
  J Biol Chem, 281, 9400-9406.  
16908625 L.Delamarre, R.Couture, I.Mellman, and E.S.Trombetta (2006).
Enhancing immunogenicity by limiting susceptibility to lysosomal proteolysis.
  J Exp Med, 203, 2049-2055.  
15861139 C.Ritter, K.Quirin, M.Kowarik, and A.Helenius (2005).
Minor folding defects trigger local modification of glycoproteins by the ER folding sensor GT.
  EMBO J, 24, 1730-1738.  
16199662 D.A.Schultz, A.M.Friedman, M.A.White, and R.O.Fox (2005).
The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A.
  Protein Sci, 14, 2862-2870.
PDB code: 1kh8
15761154 L.Delamarre, M.Pack, H.Chang, I.Mellman, and E.S.Trombetta (2005).
Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate.
  Science, 307, 1630-1634.  
14500871 A.T.Alexandrescu, and R.A.Kammerer (2003).
Structure and disorder in the ribonuclease S-peptide probed by NMR residual dipolar couplings.
  Protein Sci, 12, 2132-2140.  
12518055 J.J.Caramelo, O.A.Castro, L.G.Alonso, G.De Prat-Gay, and A.J.Parodi (2003).
UDP-Glc:glycoprotein glucosyltransferase recognizes structured and solvent accessible hydrophobic patches in molten globule-like folding intermediates.
  Proc Natl Acad Sci U S A, 100, 86-91.  
12205097 A.I.Arunkumar, S.Srisailam, T.K.Kumar, K.M.Kathir, Y.H.Chi, H.M.Wang, G.G.Chang, I.Chiu, and C.Yu (2002).
Structure and stability of an acidic fibroblast growth factor from Notophthalmus viridescens.
  J Biol Chem, 277, 46424-46432.
PDB code: 1fmm
12070144 S.Chakravarty, A.Bhinge, and R.Varadarajan (2002).
A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding.
  J Biol Chem, 277, 31345-31353.  
12324443 S.D.Stelea, and T.A.Keiderling (2002).
Pretransitional structural changes in the thermal denaturation of ribonuclease S and S protein.
  Biophys J, 83, 2259-2269.  
11914480 W.M.Vetter, D.T.Gallagher, and M.Dudley (2002).
Synchrotron white-beam X-ray topography of ribonuclease S crystals.
  Acta Crystallogr D Biol Crystallogr, 58, 579-584.  
11604523 D.D.Ojennus, M.R.Fleissner, and D.S.Wuttke (2001).
Reconstitution of a native-like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear NMR.
  Protein Sci, 10, 2162-2175.  
11170206 M.Bastos, J.H.Pease, D.E.Wemmer, K.P.Murphy, and P.R.Connelly (2001).
Thermodynamics of the helix-coil transition: Binding of S15 and a hybrid sequence, disulfide stabilized peptide to the S-protein.
  Proteins, 42, 523-530.  
11354368 S.Futaki, M.Araki, T.Kiwada, I.Nakase, and Y.Sugiura (2001).
A 'cassette' RNase: site-selective cleavage of RNA by RNase S equipped with RNA-recognition segment.
  Bioorg Med Chem Lett, 11, 1165-1168.  
10725325 E.S.Trombetta, and A.Helenius (2000).
Conformational requirements for glycoprotein reglucosylation in the endoplasmic reticulum.
  J Cell Biol, 148, 1123-1129.  
10639110 G.D.Rose (2000).
Lysozyme among the Lilliputians.
  Proc Natl Acad Sci U S A, 97, 526-528.  
11015216 G.S.Ratnaparkhi, and R.Varadarajan (2000).
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.
  Biochemistry, 39, 12365-12374.
PDB codes: 1d5d 1d5e 1d5h
10393919 G.Chakshusmathi, G.S.Ratnaparkhi, P.K.Madhu, and R.Varadarajan (1999).
Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments.
  Proc Natl Acad Sci U S A, 96, 7899-7904.  
10409822 G.S.Ratnaparkhi, and R.Varadarajan (1999).
X-ray crystallographic studies of the denaturation of ribonuclease S.
  Proteins, 36, 282-294.
PDB codes: 1cjq 1cjr
10051587 J.M.Goldberg, and R.L.Baldwin (1999).
A specific transition state for S-peptide combining with folded S-protein and then refolding.
  Proc Natl Acad Sci U S A, 96, 2019-2024.  
  9521116 A.T.Alexandrescu, K.Rathgeb-Szabo, K.Rumpel, W.Jahnke, T.Schulthess, and R.A.Kammerer (1998).
15N backbone dynamics of the S-peptide from ribonuclease A in its free and S-protein bound forms: toward a site-specific analysis of entropy changes upon folding.
  Protein Sci, 7, 389-402.  
9154942 D.D.Leonidas, R.Shapiro, L.I.Irons, N.Russo, and K.R.Acharya (1997).
Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution.
  Biochemistry, 36, 5578-5588.
PDB codes: 1afk 1afl 1afu
9057494 G.Kurapkat, P.Krüger, A.Wollmer, J.Fleischhauer, B.Kramer, E.Zobel, A.Koslowski, H.Botterweck, and R.W.Woody (1997).
Calculations of the CD spectrum of bovine pancreatic ribonuclease.
  Biopolymers, 41, 267-287.  
9354629 H.H.de Jongh, E.Goormaghtigh, and J.M.Ruysschaert (1997).
Amide-proton exchange of water-soluble proteins of different structural classes studied at the submolecular level by infrared spectroscopy.
  Biochemistry, 36, 13603-13610.  
8973167 A.A.Fedorov, D.Joseph-McCarthy, E.Fedorov, D.Sirakova, I.Graf, and S.C.Almo (1996).
Ionic interactions in crystalline bovine pancreatic ribonuclease A.
  Biochemistry, 35, 15962-15979.
PDB codes: 1rno 1rnq 1rnw 1rnx 1rny 1rnz
8873605 F.Catanzano, C.Giancola, G.Graziano, and G.Barone (1996).
Temperature-induced denaturation of ribonuclease S: a thermodynamic study.
  Biochemistry, 35, 13378-13385.  
  8897611 G.Nadig, G.S.Ratnaparkhi, R.Varadarajan, and S.Vishveshwara (1996).
Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies.
  Protein Sci, 5, 2104-2114.  
8983237 S.D.Durbin, and G.Feher (1996).
Protein crystallization.
  Annu Rev Phys Chem, 47, 171-204.  
8749854 J.Janin, and F.Rodier (1995).
Protein-protein interaction at crystal contacts.
  Proteins, 23, 580-587.  
7737987 J.S.Kim, J.Soucek, J.Matousek, and R.T.Raines (1995).
Structural basis for the biological activities of bovine seminal ribonuclease.
  J Biol Chem, 270, 10525-10530.  
7556203 P.Flecker (1995).
Template-directed protein folding into a metastable state of increased activity.
  Eur J Biochem, 232, 528-535.  
  7756988 I.Zegers, D.Maes, M.H.Dao-Thi, F.Poortmans, R.Palmer, and L.Wyns (1994).
The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.
  Protein Sci, 3, 2322-2339.
PDB codes: 1rpf 1rpg 1rph
8058892 F.M.Richards, and W.A.Lim (1993).
An analysis of packing in the protein folding problem.
  Q Rev Biophys, 26, 423-498.  
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.