spacer
spacer

PDBsum entry 1b21

Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase PDB id
1b21
Jmol
Contents
Protein chains
109 a.a. *
Metals
_ZN
Waters ×339
* Residue conservation analysis
PDB id:
1b21
Name: Hydrolase
Title: Deletion of a buried salt bridge in barnase
Structure: Protein (barnase). Chain: a, b, c. Engineered: yes. Mutation: yes
Source: Bacillus amyloliquefaciens. Organism_taxid: 1390. Cellular_location: extracellular. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.188     R-free:   0.268
Authors: C.K.Vaughan,P.Harryson,A.M.Buckle,M.Oliveberg,A.R.Fersht
Key ref: A.M.Buckle et al. (1993). Crystal structural analysis of mutations in the hydrophobic cores of barnase. J Mol Biol, 234, 847-860. PubMed id: 8254677
Date:
03-Dec-98     Release date:   09-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00648  (RNBR_BACAM) -  Ribonuclease
Seq:
Struc:
157 a.a.
109 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA binding     3 terms  

 

 
J Mol Biol 234:847-860 (1993)
PubMed id: 8254677  
 
 
Crystal structural analysis of mutations in the hydrophobic cores of barnase.
A.M.Buckle, K.Henrick, A.R.Fersht.
 
  ABSTRACT  
 
We have solved and analysed the crystal structures of five mutants in the hydrophobic core of barnase to investigate the structural basis for the contribution of hydrophobic residues and side-chain packing to the stability of globular proteins. In case ease, an amino acid side-chain has been replaced with one of smaller volume. The overall structures of four Ile-->Val mutants (residues 51, 76, 88 and 96) and one Leu-->Val mutant (residue 89) are all isomorphous with the wild-type structure. The magnitude and nature of structural shifts in the three hydrophobic core regions of barnase depend on the local environment of the substitution site, but have some features in common. (1) Side-chain atoms move to a greater extent than do main-chain atoms. (2) Repacking at the substitution site is achieved by either a rigid body shift of side-chain atoms (for Ile-->Val76 and Ile-->Val96 mutants), or by a combination of a side-chain shift and rotation (for Ile-->Val51 and Ile-->Val88 mutants). The mutated residue moves to the greatest extent, and generally in the direction of the created cavity (the largest atomic shift is 0.9 A, for Ile-->Val51). The space left behind from such shifts is not seen to be filled by neighbouring side-chains. (3) Where a cavity remains after mutation, it does not contain any solvent molecules. (4) There is no correlation between the extent of structural movements and the atomic temperature factors of atoms that have moved. (5) Structural movements are not large enough to disrupt hydrogen bonding. Valine 88, in the Ile-->Val88 mutant, is disordered and the electron density suggests several side-chain conformations. The reduction in the volumes of the cavities introduced upon mutation, due to collapse of the surrounding structure, ranges from 11% (Ile-->Val96) to 90% (Ile-->Val51).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17401432 A.C.Joerger, and A.R.Fersht (2007).
Structure-function-rescue: the diverse nature of common p53 cancer mutants.
  Oncogene, 26, 2226-2242.  
17015838 A.C.Joerger, H.C.Ang, and A.R.Fersht (2006).
Structural basis for understanding oncogenic p53 mutations and designing rescue drugs.
  Proc Natl Acad Sci U S A, 103, 15056-15061.
PDB codes: 2j1w 2j1x 2j1y 2j1z 2j20 2j21
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.  
16877708 M.Bueno, L.A.Campos, J.Estrada, and J.Sancho (2006).
Energetics of aliphatic deletions in protein cores.
  Protein Sci, 15, 1858-1872.  
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
17038664 P.Cioni (2006).
Role of protein cavities on unfolding volume change and on internal dynamics under pressure.
  Biophys J, 91, 3390-3396.  
15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
  Proteins, 59, 580-591.  
16109374 K.Kamada, and F.Hanaoka (2005).
Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin.
  Mol Cell, 19, 497-509.
PDB codes: 2a6q 2a6r 2a6s
15937899 S.Park, and J.G.Saven (2005).
Statistical and molecular dynamics studies of buried waters in globular proteins.
  Proteins, 60, 450-463.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
15557258 M.J.Lachenmann, J.E.Ladbury, X.Qian, K.Huang, R.Singh, and M.A.Weiss (2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
  Protein Sci, 13, 3115-3126.
PDB code: 1xrz
15162481 S.Ventura, and L.Serrano (2004).
Designing proteins from the inside out.
  Proteins, 56, 1.  
15096198 T.J.Magliery, and L.Regan (2004).
Combinatorial approaches to protein stability and structure.
  Eur J Biochem, 271, 1595-1608.  
12455067 R.Rodríguez-López, A.Osorio, L.Sánchez-Pulido, M.De La Hoya, A.Barroso, T.Caldés, and J.Benítez (2003).
No mutations in the XRCC2 gene in BRCA1/2-negative high-risk breast cancer families.
  Int J Cancer, 103, 136-137.  
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
12471608 T.Wang, and R.C.Wade (2003).
Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.
  Proteins, 50, 158-169.  
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.  
11847280 A.Heifetz, E.Katchalski-Katzir, and M.Eisenstein (2002).
Electrostatics in protein-protein docking.
  Protein Sci, 11, 571-587.  
11927576 J.Funahashi, K.Takano, Y.Yamagata, and K.Yutani (2002).
Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability.
  J Biol Chem, 277, 21792-21800.
PDB codes: 1gf8 1gf9 1gfa 1gfe 1gfg 1gfh 1gfj 1gfk 1gfr 1gft 1gfu 1gfv 1inu
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.  
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.  
11264576 J.W.O'Neill, D.E.Kim, D.Baker, and K.Y.Zhang (2001).
Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.
  Acta Crystallogr D Biol Crystallogr, 57, 480-487.
PDB codes: 1hz5 1hz6
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.  
11112523 E.J.Sundberg, M.Urrutia, B.C.Braden, J.Isern, D.Tsuchiya, B.A.Fields, E.L.Malchiodi, J.Tormo, F.P.Schwarz, and R.A.Mariuzza (2000).
Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.
  Biochemistry, 39, 15375-15387.
PDB codes: 1g7h 1g7i 1g7j 1g7l 1g7m
10656266 H.Kono, M.Saito, and A.Sarai (2000).
Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations.
  Proteins, 38, 197-209.  
11087397 J.Funahashi, K.Takano, Y.Yamagata, and K.Yutani (2000).
Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions.
  Biochemistry, 39, 14448-14456.
PDB codes: 1gay 1gb0 1gb2 1gb3 1gb5 1gb6 1gb7 1gb8 1gb9 1gbo 1gbw 1gbx 1gby 1gbz
10654936 P.V.Nikolova, K.B.Wong, B.DeDecker, J.Henckel, and A.R.Fersht (2000).
Mechanism of rescue of common p53 cancer mutations by second-site suppressor mutations.
  EMBO J, 19, 370-378.  
  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.  
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
10373011 R.Loris, U.Langhorst, S.De Vos, K.Decanniere, J.Bouckaert, D.Maes, T.R.Transue, and J.Steyaert (1999).
Conserved water molecules in a large family of microbial ribonucleases.
  Proteins, 36, 117-134.
PDB codes: 1bu4 2bu4 3bu4 4bu4 5bu4
9484240 V.De Filippis, F.De Antoni, M.Frigo, P.Polverino de Laureto, and A.Fontana (1998).
Enhanced protein thermostability by Ala-->Aib replacement.
  Biochemistry, 37, 1686-1696.  
9649316 Y.Yamagata, M.Kubota, Y.Sumikawa, J.Funahashi, K.Takano, S.Fujii, and K.Yutani (1998).
Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six tyrosine --> phenylalanine mutants.
  Biochemistry, 37, 9355-9362.
PDB codes: 1wqm 1wqn 1wqo 1wqp 1wqq 1wqr
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.  
9020766 K.Takano, Y.Yamagata, S.Fujii, and K.Yutani (1997).
Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants.
  Biochemistry, 36, 688-698.
PDB codes: 1oub 1ouc 1oud 1oue 1ouf 1oug 1ouh 1oui 1ouj
9129797 R.R.Gabdoulline, and R.C.Wade (1997).
Simulation of the diffusional association of barnase and barstar.
  Biophys J, 72, 1917-1929.  
8605178 A.M.Buckle, P.Cramer, and A.R.Fersht (1996).
Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities.
  Biochemistry, 35, 4298-4305.
PDB codes: 1brh 1bri 1brj 1brk
8952503 B.A.Fields, F.A.Goldbaum, W.Dall'Acqua, E.L.Malchiodi, A.Cauerhff, F.P.Schwarz, X.Ysern, R.J.Poljak, and R.A.Mariuzza (1996).
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
  Biochemistry, 35, 15494-15503.
PDB codes: 1kip 1kiq 1kir
  8844858 E.S.Eberhardt, P.K.Wittmayer, B.M.Templer, and R.T.Raines (1996).
Contribution of a tyrosine side chain to ribonuclease A catalysis and stability.
  Protein Sci, 5, 1697-1703.  
8639631 M.Oliveberg, and A.R.Fersht (1996).
New approach to the study of transient protein conformations: the formation of a semiburied salt link in the folding pathway of barnase.
  Biochemistry, 35, 6795-6805.  
7615544 S.Ganguli, H.Wang, P.Matsumura, and K.Volz (1995).
Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.1-A structure of a threonine to isoleucine mutant at position 87 of CheY.
  J Biol Chem, 270, 17386-17393.
PDB code: 1vlz
7765172 E.P.Baldwin, and B.W.Matthews (1994).
Core-packing constraints, hydrophobicity and protein design.
  Curr Opin Biotechnol, 5, 396-402.  
7922041 Y.Harpaz, M.Gerstein, and C.Chothia (1994).
Volume changes on protein folding.
  Structure, 2, 641-649.  
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.