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PDBsum entry 1gfr

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protein metals links
Hydrolase PDB id
1gfr
Jmol
Contents
Protein chain
130 a.a. *
Metals
_NA
Waters ×288
* Residue conservation analysis
PDB id:
1gfr
Name: Hydrolase
Title: Crystal structure of mutant human lysozyme substituted at the surface positions
Structure: Lysozyme. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
1.80Å     R-factor:   0.179    
Authors: J.Funahashi,K.Takano,Y.Yamagata,K.Yutani
Key ref:
J.Funahashi et al. (2000). Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions. Biochemistry, 39, 14448-14456. PubMed id: 11087397 DOI: 10.1021/bi0015717
Date:
04-Dec-00     Release date:   27-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61626  (LYSC_HUMAN) -  Lysozyme C
Seq:
Struc:
148 a.a.
130 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1021/bi0015717 Biochemistry 39:14448-14456 (2000)
PubMed id: 11087397  
 
 
Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions.
J.Funahashi, K.Takano, Y.Yamagata, K.Yutani.
 
  ABSTRACT  
 
To evaluate the contribution of the amino acid residues on the surface of a protein to its stability, a series of hydrophobic mutant human lysozymes (Val to Gly, Ala, Leu, Ile, Met, and Phe) modified at three different positions on the surface, which are located in the alpha-helix (Val 110), the beta-sheet (Val 2), and the loop (Val 74), were constructed. Their thermodynamic parameters of denaturation and crystal structures were examined by calorimetry and by X-ray crystallography at 100 K, respectively. Differences in the denaturation Gibbs energy change between the wild-type and the hydrophobic mutant proteins ranged from 4.6 to -9.6 kJ/mol, 2.7 to -1.5 kJ/mol, and 3.6 to -0.2 kJ/mol at positions 2, 74, and 110, respectively. The identical substitution at different positions and different substitutions at the same position resulted in different degrees of stabilization. Changes in the stability of the mutant proteins could be evaluated by a unique equation considering the conformational changes due to the substitutions [Funahashi et al. (1999) Protein Eng. 12, 841-850]. For this calculation, secondary structural propensities were newly considered. However, some mutant proteins were not adapted to the equation. The hydration structures around the mutation sites of the exceptional mutant proteins were affected due to the substitutions. The stability changes in the exceptional mutant proteins could be explained by the formation or destruction of the hydration structures. These results suggest that the hydration structure mediated via hydrogen bonds covering the protein surface plays an important role in the conformational stability of the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20596542 A.Bhardwaj, S.Leelavathi, S.Mazumdar-Leighton, A.Ghosh, S.Ramakumar, and V.S.Reddy (2010).
The critical role of N- and C-terminal contact in protein stability and folding of a family 10 xylanase under extreme conditions.
  PLoS One, 5, e11347.  
18725971 A.Bharadwaj, S.Leelavathi, S.Mazumdar-Leighton, A.Ghosh, S.Ramakumar, and V.S.Reddy (2008).
The critical role of partially exposed N-terminal valine residue in stabilizing GH10 xylanase from Bacillus sp.NG-27 under poly-extreme conditions.
  PLoS ONE, 3, e3063.  
17377990 L.Fernández, J.Caballero, J.I.Abreu, and M.Fernández (2007).
Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants.
  Proteins, 67, 834-852.  
16441658 J.R.Kumita, R.J.Johnson, M.J.Alcocer, M.Dumoulin, F.Holmqvist, M.G.McCammon, C.V.Robinson, D.B.Archer, and C.M.Dobson (2006).
Impact of the native-state stability of human lysozyme variants on protein secretion by Pichia pastoris.
  FEBS J, 273, 711-720.  
16467302 K.Miyazaki, M.Takenouchi, H.Kondo, N.Noro, M.Suzuki, and S.Tsuda (2006).
Thermal stabilization of Bacillus subtilis family-11 xylanase by directed evolution.
  J Biol Chem, 281, 10236-10242.
PDB codes: 2dcy 2dcz
15819891 Y.S.Yun, G.H.Nam, Y.G.Kim, B.H.Oh, and K.Y.Choi (2005).
Small exterior hydrophobic cluster contributes to conformational stability and steroid binding in ketosteroid isomerase from Pseudomonas putida biotype B.
  FEBS J, 272, 1999-2011.
PDB code: 1w6y
11959988 A.R.Viguera, C.Vega, and L.Serrano (2002).
Unspecific hydrophobic stabilization of folding transition states.
  Proc Natl Acad Sci U S A, 99, 5349-5354.
PDB code: 1hd3
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
11599030 K.Takano, Y.Yamagata, and K.Yutani (2001).
Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein.
  Proteins, 45, 274-280.
PDB codes: 1ip1 1ip2 1ip3 1ip4 1ip5 1ip6 1ip7
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.