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PDBsum entry 1bnr
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Microbial ribonuclease PDB id
1bnr

 

 

 

 

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Contents
Protein chain
110 a.a. *
* Residue conservation analysis
PDB id:
1bnr
Name: Microbial ribonuclease
Title: Barnase
Structure: Barnase (g specific endonuclease). Chain: a. Engineered: yes. Other_details: nmr, 20 structures
Source: Bacillus amyloliquefaciens. Organism_taxid: 1390. Gene: barnase. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: M.Bycroft
Key ref:
M.Bycroft et al. (1991). Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy. Biochemistry, 30, 8697-8701. PubMed id: 1888730 DOI: 10.1021/bi00099a030
Date:
31-Mar-95     Release date:   31-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P00648  (RNBR_BACAM) -  Ribonuclease from Bacillus amyloliquefaciens
Seq:
Struc: 		157 a.a.
110 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/bi00099a030 Biochemistry 30:8697-8701 (1991)
PubMed id: 1888730  
 
 
Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy.
M.Bycroft, S.Ludvigsen, A.R.Fersht, F.M.Poulsen.
 
  ABSTRACT  
 
The solution conformation of the ribonuclease barnase has been determined by using 1H nuclear magnetic resonance (NMR) spectroscopy. The 20 structures were calculated by using 853 interproton distance restraints obtained from analyses of two-dimensional nuclear Overhauser spectra, 72 phi and 53 chi 1 torsion angle restraints, and 17 hydrogen-bond distance restraints. The calculated structures contain two alpha-helices (residues 6-18 and 26-34) and a five-stranded antiparallel beta-sheet (residues 50-55, 70-75, 85-91, 94-101, and 105-108). The core of the protein is formed by the packing of one of the alpha-helices (residues 6-18) onto the beta-sheet. The average RMS deviation between the calculated structures and the mean structure is 1.11 A for the backbone atoms and 1.75 A for all atoms. The protein is least well-defined in the N-terminal region and in three large loops. When these regions are excluded, the average RMS deviation between the calculated structures and the mean structure for residues 5-34, 50-56, 71-76, 85-109 is 0.62 A for the backbone atoms and 1.0 A for all atoms. The NMR-derived structure has been compared with the crystal structure of barnase [Mauguen et al. (1982) Nature (London) 297, 162-164].
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18979065 M.Cioffi, C.A.Hunter, M.J.Packer, M.J.Pandya, and M.P.Williamson (2009).
Use of quantitative (1)H NMR chemical shift changes for ligand docking into barnase.
  J Biomol NMR, 43, 11-19.  
19597264 S.A.Menor, A.M.de Graff, and M.F.Thorpe (2009).
Hierarchical plasticity from pair distance fluctuations.
  Phys Biol, 6, 36017.  
18247351 G.Morra, and G.Colombo (2008).
Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins.
  Proteins, 72, 660-672.  
18441234 Y.Urakubo, T.Ikura, and N.Ito (2008).
Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation.
  Protein Sci, 17, 1055-1065.
PDB code: 2za4
16550537 K.Ohno, and M.Sakurai (2006).
Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins.
  J Comput Chem, 27, 906-916.  
16791739 N.Powers, and J.H.Jensen (2006).
Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.
  J Biomol NMR, 35, 39-51.  
16280618 S.Wells, S.Menor, B.Hespenheide, and M.F.Thorpe (2005).
Constrained geometric simulation of diffusive motion in proteins.
  Phys Biol, 2, S127-S136.  
14691227 G.Tiana, F.Simona, G.M.De Mori, R.A.Broglia, and G.Colombo (2004).
Understanding the determinants of stability and folding of small globular proteins from their energetics.
  Protein Sci, 13, 113-124.  
15211510 J.Giraldo, L.De Maria, and S.J.Wodak (2004).
Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase.
  Proteins, 56, 261-276.  
15215525 K.R.Somers, P.Krüger, S.Bucikiewicz, M.De Maeyer, Y.Engelborghs, and A.Ceulemans (2004).
Protein simulations: the absorption spectrum of barnase point mutants.
  Protein Sci, 13, 1823-1831.  
12778129 V.Daggett, and A.Fersht (2003).
The present view of the mechanism of protein folding.
  Nat Rev Mol Cell Biol, 4, 497-502.  
12517448 V.Daggett, and A.R.Fersht (2003).
Is there a unifying mechanism for protein folding?
  Trends Biochem Sci, 28, 18-25.  
11746702 A.A.Gorfe, P.Ferrara, A.Caflisch, D.N.Marti, H.R.Bosshard, and I.Jelesarov (2002).
Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase.
  Proteins, 46, 41-60.  
11914482 C.K.Vaughan, P.Harryson, A.M.Buckle, and A.R.Fersht (2002).
A structural double-mutant cycle: estimating the strength of a buried salt bridge in barnase.
  Acta Crystallogr D Biol Crystallogr, 58, 591-600.
PDB codes: 1b20 1b21 1b2x 1b2z
12324397 R.E.Georgescu, E.G.Alexov, and M.R.Gunner (2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
  Biophys J, 83, 1731-1748.  
11835500 S.B.Nolde, A.S.Arseniev, V.Y.Orekhov, and M.Billeter (2002).
Essential domain motions in barnase revealed by MD simulations.
  Proteins, 46, 250-258.  
11169386 K.Takahashi, T.Noguti, H.Hojo, T.Ohkubo, and M.Gō (2001).
Conformational characterization of designed minibarnase.
  Biopolymers, 58, 260-267.  
11566804 R.B.Best, B.Li, A.Steward, V.Daggett, and J.Clarke (2001).
Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation.
  Biophys J, 81, 2344-2356.  
  11206061 J.Clarke, A.M.Hounslow, C.J.Bond, A.R.Fersht, and V.Daggett (2000).
The effects of disulfide bonds on the denatured state of barnase.
  Protein Sci, 9, 2394-2404.  
10806383 J.L.Neira, E.Vázquez, and A.R.Fersht (2000).
Stability and folding of the protein complexes of barnase.
  Eur J Biochem, 267, 2859-2870.  
11106501 V.Gaponenko, A.Dvoretsky, C.Walsby, B.M.Hoffman, and P.R.Rosevear (2000).
Calculation of z-coordinates and orientational restraints using a metal binding tag.
  Biochemistry, 39, 15217-15224.  
  10716182 V.Gaponenko, J.W.Howarth, L.Columbus, G.Gasmi-Seabrook, J.Yuan, W.L.Hubbell, and P.R.Rosevear (2000).
Protein global fold determination using site-directed spin and isotope labeling.
  Protein Sci, 9, 302-309.  
10378267 A.Caflisch, and M.Karplus (1999).
Structural details of urea binding to barnase: a molecular dynamics analysis.
  Structure, 7, 477-488.  
10089345 C.Martin, V.Richard, M.Salem, R.Hartley, and Y.Mauguen (1999).
Refinement and structural analysis of barnase at 1.5 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 386-398.
PDB code: 1a2p
9391038 C.J.Bond, K.B.Wong, J.Clarke, A.R.Fersht, and V.Daggett (1997).
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway.
  Proc Natl Acad Sci U S A, 94, 13409-13413.  
9129797 R.R.Gabdoulline, and R.C.Wade (1997).
Simulation of the diffusional association of barnase and barstar.
  Biophys J, 72, 1917-1929.  
  8520478 P.L.Wintrode, Y.V.Griko, and P.L.Privalov (1995).
Structural energetics of barstar studied by differential scanning microcalorimetry.
  Protein Sci, 4, 1528-1534.  
7937096 A.A.Schulga, I.V.Levichkin, F.T.Kurkbanov, A.L.Okorokov, G.E.Pozmogova, and M.P.Kirpichnikov (1994).
An approach to construction of hybrid polypeptide molecules--homologue recombination method.
  Nucleic Acids Res, 22, 3808-3810.  
8127876 A.Caflisch, and M.Karplus (1994).
Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase.
  Proc Natl Acad Sci U S A, 91, 1746-1750.  
  8407848 S.Mathur, V.J.Cannistraro, and D.Kennell (1993).
Identification of an intracellular pyrimidine-specific endoribonuclease from Bacillus subtilis.
  J Bacteriol, 175, 6717-6720.  
8356030 T.Ikura, N.Go, D.Kohda, F.Inagaki, H.Yanagawa, M.Kawabata, S.Kawabata, S.Iwanaga, T.Noguti, and M.Go (1993).
Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation.
  Proteins, 16, 341-356.  
16100951 V.Guillet, A.Lapthorn, R.W.Hartley, and Y.Mauguen (1993).
Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar.
  Structure, 1, 165-176.
PDB code: 1bgs
1470680 M.Billeter (1992).
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
  Q Rev Biophys, 25, 325-377.  
1392567 S.Ludvigsen, and F.M.Poulsen (1992).
Positive theta-angles in proteins by nuclear magnetic resonance spectroscopy.
  J Biomol NMR, 2, 227-233.  
1368432 W.J.Chazin (1992).
NMR structures and methodology.
  Curr Opin Biotechnol, 3, 326-332.  
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.

 

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