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PDBsum entry 1c54

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protein links
Hydrolase PDB id
1c54
Jmol
Contents
Protein chain
96 a.a. *
* Residue conservation analysis
PDB id:
1c54
Name: Hydrolase
Title: Solution structure of ribonuclease sa
Structure: Ribonuclease sa. Chain: a. Engineered: yes
Source: Streptomyces aureofaciens. Organism_taxid: 1894. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: D.V.Laurents,J.M.Canadillas-Perez,J.Santoro,D.Schell, C.N.Pace,M.Rico,M.Bruix
Key ref:
D.Laurents et al. (2001). Solution structure and dynamics of ribonuclease Sa. Proteins, 44, 200-211. PubMed id: 11455593 DOI: 10.1002/prot.1085
Date:
22-Oct-99     Release date:   28-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05798  (RNSA_STRAU) -  Guanyl-specific ribonuclease Sa
Seq:
Struc:
96 a.a.
96 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.3  - Ribonuclease T(1).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in G-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
DOI no: 10.1002/prot.1085 Proteins 44:200-211 (2001)
PubMed id: 11455593  
 
 
Solution structure and dynamics of ribonuclease Sa.
D.Laurents, J.M.Pérez-Cañadillas, J.Santoro, M.Rico, D.Schell, C.N.Pace, M.Bruix.
 
  ABSTRACT  
 
We have used NMR methods to characterize the structure and dynamics of ribonuclease Sa in solution. The solution structure of RNase Sa was obtained using the distance constraints provided by 2,276 NOEs and the C6-C96 disulfide bond. The 40 resulting structures are well determined; their mean pairwise RMSD is 0.76 A (backbone) and 1.26 A (heavy atoms). The solution structures are similar to previously determined crystal structures, especially in the secondary structure, but exhibit new features: the loop composed of Pro 45 to Ser 48 adopts distinct conformations and the rings of tyrosines 51, 52, and 55 have reduced flipping rates. Amide protons with greatly reduced exchange rates are found predominantly in interior beta-strands and the alpha-helix, but also in the external 3/10 helix and edge beta-strand linked by the disulfide bond. Analysis of (15)N relaxation experiments (R1, R2, and NOE) at 600 MHz revealed five segments, consisting of residues 1-5, 28-31, 46-50, 60-65, 74-77, retaining flexibility in solution. The change in conformation entropy for RNase SA folding is smaller than previously believed, since the native protein is more flexible in solution than in a crystal.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Cross-eyed stereo view of the ensemble of the 40 superimposed solution structures is plotted, with the 3/10 and -helices (green), the -sheet (blue), flexible loops (red), and residues 45-48, which have three conformational families (brown).
Figure 5.
Figure 5. Typical relaxation decay curves. A: R1. B: R2. Val 2 ( , flexible N-terminus), Leu 11 ( , 3/10 helix), Leu 21 ( , -helix), Ile 70 ( , -sheet) relaxation are shown for R1 (A) and R2 (B). Solid lines, fit of a monoexponential decay function.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 44, 200-211) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20197040 A.Kuzmanic, and B.Zagrovic (2010).
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.
  Biophys J, 98, 861-871.  
19558492 V.Bauerová-Hlinková, R.Dvorský, D.Perecko, F.Povazanec, and J.Sevcík (2009).
Structure of RNase Sa2 complexes with mononucleotides--new aspects of catalytic reaction and substrate recognition.
  FEBS J, 276, 4156-4168.
PDB codes: 3d4a 3d5g 3d5i 3dgy 3dh2
18065473 R.W.Alston, M.Lasagna, G.R.Grimsley, J.M.Scholtz, G.D.Reinhart, and C.N.Pace (2008).
Tryptophan fluorescence reveals the presence of long-range interactions in the denatured state of ribonuclease Sa.
  Biophys J, 94, 2288-2296.  
15306378 C.N.Pace, S.Treviño, E.Prabhakaran, and J.M.Scholtz (2004).
Protein structure, stability and solubility in water and other solvents.
  Philos Trans R Soc Lond B Biol Sci, 359, 1225.  
15377518 R.W.Alston, L.Urbanikova, J.Sevcik, M.Lasagna, G.D.Reinhart, J.M.Scholtz, and C.N.Pace (2004).
Contribution of single tryptophan residues to the fluorescence and stability of ribonuclease Sa.
  Biophys J, 87, 4036-4047.
PDB codes: 1t2h 1t2i
14500895 G.I.Yakovlev, V.A.Mitkevich, K.L.Shaw, S.Trevino, S.Newsom, C.N.Pace, and A.A.Makarov (2003).
Contribution of active site residues to the activity and thermal stability of ribonuclease Sa.
  Protein Sci, 12, 2367-2373.  
12799387 K.Takano, J.M.Scholtz, J.C.Sacchettini, and C.N.Pace (2003).
The contribution of polar group burial to protein stability is strongly context-dependent.
  J Biol Chem, 278, 31790-31795.
PDB codes: 1uci 1ucj 1uck 1ucl
11835498 E.E.Lattman, and D.E.Draper (2002).
Review of the sixth Annual Johns Hopkins Folding Meeting.
  Proteins, 46, 237-242.  
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.