PDBsum entry 1rbe

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Hydrolase(phosphoric diester,RNA) PDB id
Protein chains
16 a.a.
104 a.a. *
Waters ×63
* Residue conservation analysis
PDB id:
Name: Hydrolase(phosphoric diester,RNA)
Title: Crystallographic structures of ribonuclease s variants with nonpolar substitution at position 13: packing and cavities
Structure: Ribonuclease s (s-peptide). Chain: s. Engineered: yes. Ribonuclease s (s-protein). Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Dimer (from PQS)
1.75Å     R-factor:   0.186    
Authors: R.Varadarajan,F.M.Richards
Key ref:
R.Varadarajan and F.M.Richards (1992). Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities. Biochemistry, 31, 12315-12327. PubMed id: 1463720 DOI: 10.1021/bi00164a005
12-Jun-92     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
16 a.a.*
Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains S, A: E.C.  - 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!
  Biochemical function     nucleic acid binding     1 term  


DOI no: 10.1021/bi00164a005 Biochemistry 31:12315-12327 (1992)
PubMed id: 1463720  
Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities.
R.Varadarajan, F.M.Richards.
Seven hydrophobic residues ranging in size from glycine to phenylalanine have been substituted for the wild-type methionine residue at position 13 in a 15-residue truncated version (S15) of S-peptide, the small component of ribonuclease S. Complexes of both S-15 and the seven variants with S-protein yielded isomorphous crystals. The structures of all eight complexes have been refined to final R-factors in the range of 17-19%. [See Kim, E. E. Varadarajan, R., Wyckoff, H. W., and Richards, F. M. (1992) Biochemistry (preceding paper in this issue) for the description of the reference S-15 complex.] Multiple side-chain conformations were seen for six residues in all of the complexes and for two to three additional residues in at least some of the complexes. Three of the complexes, Gly, Ala, and alpha-amino-n-butyric acid (ANB), contained a single water molecule in the cavity near residue 13 that makes three hydrogen bonds to protein atoms. Although space is available, no evidence for additional water in this region, ordered or disordered, was found. The atoms in the cavity wall tend to shrink the cavity by moving in on the small residues and to swell the cavity by moving out for the larger Phe substitution. A swelling seen with leucine was attributed to a shape effect since Leu, Ile, and Met all have the same volume. A slight volume contraction of the collection of interior residues outside of the region of position 13 was also noted. (All changes noted are in the direction to maintain a constant packing density averaged over the whole protein.) Leu51, a surface hydrophobic residue, moved considerably in the G, A, and ANB complexes in directionswhich would tend to decrease the cavity volume. The only other major change in position, 1.5 A, was the 66-69 loop, which is about 25 A from position 13. His12, Phe120, and Asp121 appear to be involved in this movement, but the connection with position 13 is not clear at all. The thermodynamic data on the association reaction for all of these complexes have been previously reported [Connelly, P. R., Varadarajan, R., Sturtevant, J. M., & Richards, F. M. (1990) Biochemistry 29, 6108-6114; Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426]. Some comments are offered on our initial attempts to correlate the structural changes with the changes in the thermodynamic parameters.(ABSTRACT TRUNCATED AT 400 WORDS)

Literature references that cite this PDB file's key reference

  PubMed id Reference
19373927 R.Vilà, A.Benito, M.Ribó, and M.Vilanova (2009).
Mapping the stability clusters in bovine pancreatic ribonuclease A.
  Biopolymers, 91, 1038-1047.  
17868092 G.R.Marshall, J.A.Feng, and D.J.Kuster (2008).
Back to the future: ribonuclease A.
  Biopolymers, 90, 259-277.  
17179045 M.L.Quillin, P.T.Wingfield, and B.W.Matthews (2006).
Determination of solvent content in cavities in IL-1beta using experimentally phased electron density.
  Proc Natl Acad Sci U S A, 103, 19749-19753.
PDB code: 2nvh
15794557 A.Mahn, G.Zapata-Torres, and J.A.Asenjo (2005).
A theory of protein-resin interaction in hydrophobic interaction chromatography.
  J Chromatogr A, 1066, 81-88.  
12581214 P.Pattanaik, G.Ravindra, C.Sengupta, K.Maithal, P.Balaram, and H.Balaram (2003).
Unusual fluorescence of W168 in Plasmodium falciparum triosephosphate isomerase, probed by single-tryptophan mutants.
  Eur J Biochem, 270, 745-756.  
11939594 O.V.Tsodikov, M.T.Record, and Y.V.Sergeev (2002).
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
  J Comput Chem, 23, 600-609.  
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.  
9890931 B.Gopal, S.S.Ray, R.S.Gokhale, H.Balaram, M.R.Murthy, and P.Balaram (1999).
Cavity-creating mutation at the dimer interface of Plasmodium falciparum triosephosphate isomerase: restoration of stability by disulfide cross-linking of subunits.
  Biochemistry, 38, 478-486.  
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.  
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.  
10425675 S.Chakravarty, and R.Varadarajan (1999).
Residue depth: a novel parameter for the analysis of protein structure and stability.
  Structure, 7, 723-732.  
10090281 V.Gupta, S.Muyldermans, L.Wyns, and D.M.Salunke (1999).
The crystal structure of recombinant rat pancreatic RNase A.
  Proteins, 35, 1.
PDB code: 1rra
  9514271 J.Xu, W.A.Baase, E.Baldwin, and B.W.Matthews (1998).
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect.
  Protein Sci, 7, 158-177.
PDB codes: 235l 236l 237l 238l 239l 240l 241l 242l 243l 244l 245l 246l 247l 248l 249l 250l 251l
9228039 A.Akasako, M.Haruki, M.Oobatake, and S.Kanaya (1997).
Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core.
  J Biol Chem, 272, 18686-18693.  
  9385633 A.C.Wallace, N.Borkakoti, and J.M.Thornton (1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
  Protein Sci, 6, 2308-2323.  
9220973 M.M.Lopez, and D.Kosk-Kosicka (1997).
Entropy-driven interactions of anesthetics with membrane proteins.
  Biochemistry, 36, 8864-8872.  
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.  
  8880902 I.Vainshtein, A.Atrazhev, S.H.Eom, J.F.Elliott, D.S.Wishart, and B.A.Malcolm (1996).
Peptide rescue of an N-terminal truncation of the Stoffel fragment of taq DNA polymerase.
  Protein Sci, 5, 1785-1792.  
8946852 J.R.Tame, S.H.Sleigh, A.J.Wilkinson, and J.E.Ladbury (1996).
The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.
  Nat Struct Biol, 3, 998.
PDB codes: 1jet 1jeu 1jev
8943034 R.Varadarajan, H.A.Nagarajaram, and C.Ramakrishnan (1996).
A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence.
  Proc Natl Acad Sci U S A, 93, 13908-13913.  
7667303 P.B.Harbury, B.Tidor, and P.S.Kim (1995).
Repacking protein cores with backbone freedom: structure prediction for coiled coils.
  Proc Natl Acad Sci U S A, 92, 8408-8412.  
8519982 V.Helms, and R.C.Wade (1995).
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.
  Biophys J, 69, 810-824.  
7765172 E.P.Baldwin, and B.W.Matthews (1994).
Core-packing constraints, hydrophobicity and protein design.
  Curr Opin Biotechnol, 5, 396-402.  
  7920265 S.Bromberg, and K.A.Dill (1994).
Side-chain entropy and packing in proteins.
  Protein Sci, 3, 997.  
  8142897 V.S.deMel, M.S.Doscher, M.A.Glinn, P.D.Martin, M.L.Ram, and B.F.Edwards (1994).
Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases.
  Protein Sci, 3, 39-50.
PDB codes: 1ssa 1ssb
8278404 W.A.Lim, A.Hodel, R.T.Sauer, and F.M.Richards (1994).
The crystal structure of a mutant protein with altered but improved hydrophobic core packing.
  Proc Natl Acad Sci U S A, 91, 423-427.
PDB code: 1lli
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.