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PDBsum entry 1ouc
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Hydrolase (o-glycosyl) PDB id
1ouc

 

 

 

 

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Contents
Protein chain
130 a.a. *
Metals
_NA
Waters ×206
* Residue conservation analysis
PDB id:
1ouc
Name: Hydrolase (o-glycosyl)
Title: Contribution of hydrophobic residues to the stability of human lysozyme: x-ray structure of the v110a mutant
Structure: Lysozyme. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: human lysozyme with val 110. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
1.80Å     R-factor:   0.153    
Authors: K.Takano,Y.Yamagata,S.Fujii,K.Yutani
Key ref:
K.Takano et al. (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. PubMed id: 9020766 DOI: 10.1021/bi9621829
Date:
23-Aug-96     Release date:   12-Feb-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61626  (LYSC_HUMAN) -  Lysozyme C from Homo sapiens
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.

 

 
DOI no: 10.1021/bi9621829 Biochemistry 36:688-698 (1997)
PubMed id: 9020766  
 
 
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.
K.Takano, Y.Yamagata, S.Fujii, K.Yutani.
 
  ABSTRACT  
 
To clarify the contribution of the hydrophobic effect to the conformational stability of human lysozyme, a series of Val to Ala mutants were constructed. The thermodynamic parameters for the denaturation of these nine mutant proteins were determined using differential scanning calorimetry (DSC), and the crystal structures were solved at high resolution. The denaturation Gibbs energy (delta delta G) and enthalpy (delta delta H) values of the mutant proteins ranged from +2.2 to- 6.3 kJ/mol and from +7 to -17 kJ/mol, respectively. The structural analyses showed that the mutation site and/or the residues around it in some proteins shifted toward the created cavity, and the substitutions affected not only the mutations site but also other parts far from the site, although the structural changes were not as great. Correlation between the changes in the thermodynamic parameters and the structural features of mutant proteins was examined, including the five Ile to Val mutant human lysozymes [Takano et al. (1995) J. Mol. Biol. 254, 62-76]. There was no simple general correlation between delta delta G and the changes in hydrophobic surface area exposed upon denaturation (delta delta ASAHP). We found only a new correlation between the delta delta G and delta delta ASAHP of all of the hydrophobic residues if the effect of the secondary structure propensity was taken into account.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21119929 P.Gill, T.T.Moghadam, and B.Ranjbar (2010).
Differential scanning calorimetry techniques: applications in biology and nanoscience.
  J Biomol Tech, 21, 167-193.  
19399254 A.Mukaiyama, and K.Takano (2009).
Slow unfolding of monomeric proteins from hyperthermophiles with reversible unfolding.
  Int J Mol Sci, 10, 1369-1385.  
18785686 F.Cui, L.Qin, G.Zhang, X.Yao, and B.Lei (2008).
Study of the interaction of aglycon of daunorubicin with human serum albumin by spectroscopy and modeling.
  Macromol Biosci, 8, 1079-1089.  
17603074 D.W.Sammond, Z.M.Eletr, C.Purbeck, R.J.Kimple, D.P.Siderovski, and B.Kuhlman (2007).
Structure-based protocol for identifying mutations that enhance protein-protein binding affinities.
  J Mol Biol, 371, 1392-1404.
PDB code: 2om2
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.  
17523191 M.Bueno, C.J.Camacho, and J.Sancho (2007).
SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles.
  Proteins, 68, 850-862.  
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.  
16453276 K.Saraboji, M.M.Gromiha, and M.N.Ponnuswamy (2006).
Average assignment method for predicting the stability of protein mutants.
  Biopolymers, 82, 80-92.  
16877708 M.Bueno, L.A.Campos, J.Estrada, and J.Sancho (2006).
Energetics of aliphatic deletions in protein cores.
  Protein Sci, 15, 1858-1872.  
17038664 P.Cioni (2006).
Role of protein cavities on unfolding volume change and on internal dynamics under pressure.
  Biophys J, 91, 3390-3396.  
16055541 Y.Harano, and M.Kinoshita (2005).
Translational-entropy gain of solvent upon protein folding.
  Biophys J, 89, 2701-2710.  
15698573 Y.Li, Y.Huang, C.P.Swaminathan, S.J.Smith-Gill, and R.A.Mariuzza (2005).
Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces.
  Structure, 13, 297-307.
PDB codes: 1xgp 1xgq 1xgr 1xgt 1xgu
12837777 Z.Xu, Y.Liu, Y.Yang, W.Jiang, E.Arnold, and J.Ding (2003).
Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability.
  J Bacteriol, 185, 4038-4049.
PDB code: 1nfg
12142453 A.L.Lomize, M.Y.Reibarkh, and I.D.Pogozheva (2002).
Interatomic potentials and solvation parameters from protein engineering data for buried residues.
  Protein Sci, 11, 1984-2000.  
11742124 E.Chatani, R.Hayashi, H.Moriyama, and T.Ueki (2002).
Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 A resolution.
  Protein Sci, 11, 72-81.
PDB codes: 1eic 1eid 1eie 1fs3
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
12115138 M.M.Gromiha, M.Oobatake, H.Kono, H.Uedaira, and A.Sarai (2002).
Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations.
  Biopolymers, 64, 210-220.  
11173468 C.Qu, S.Akanuma, N.Tanaka, H.Moriyama, and T.Oshima (2001).
Design, X-ray crystallography, molecular modelling and thermal stability studies of mutant enzymes at site 172 of 3-isopropylmalate dehydrogenase from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 57, 225-232.
PDB codes: 1g2u 1gc8 1gc9
11294653 K.Takano, Y.Yamagata, and K.Yutani (2001).
Contribution of polar groups in the interior of a protein to the conformational stability.
  Biochemistry, 40, 4853-4858.
PDB codes: 1gev 1gez 1gf0 1gf3 1gf4 1gf5 1gf6 1gf7
11455596 K.Takano, Y.Yamagata, and K.Yutani (2001).
Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme.
  Proteins, 44, 233-243.
PDB codes: 1gdw 1gdx 1ge0 1ge1 1ge2 1ge3 1ge4
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
11420436 V.V.Loladze, D.N.Ermolenko, and G.I.Makhatadze (2001).
Heat capacity changes upon burial of polar and nonpolar groups in proteins.
  Protein Sci, 10, 1343-1352.  
10813830 A.Rajpal, and J.F.Kirsch (2000).
Role of the minor energetic determinants of chicken egg white lysozyme (HEWL) to the stability of the HEWL.antibody scFv-10 complex.
  Proteins, 40, 49-57.  
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
10734064 F.Gómez-Gallego, A.Garrido-Pertierra, and J.M.Bautista (2000).
Structural defects underlying protein dysfunction in human glucose-6-phosphate dehydrogenase A(-) deficiency.
  J Biol Chem, 275, 9256-9262.  
11015216 G.S.Ratnaparkhi, and R.Varadarajan (2000).
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.
  Biochemistry, 39, 12365-12374.
PDB codes: 1d5d 1d5e 1d5h
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
11015217 K.Takano, K.Tsuchimori, Y.Yamagata, and K.Yutani (2000).
Contribution of salt bridges near the surface of a protein to the conformational stability.
  Biochemistry, 39, 12375-12381.
PDB codes: 1eq4 1eq5 1eqe
10913274 K.Takano, Y.Yamagata, and K.Yutani (2000).
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme.
  Biochemistry, 39, 8655-8665.
PDB codes: 1di3 1di4 1di5 1gaz
10956017 S.T.Thomas, and G.I.Makhatadze (2000).
Contribution of the 30/36 hydrophobic contact at the C-terminus of the alpha-helix to the stability of the ubiquitin molecule.
  Biochemistry, 39, 10275-10283.  
10561612 K.Takano, K.Tsuchimori, Y.Yamagata, and K.Yutani (1999).
Effect of foreign N-terminal residues on the conformational stability of human lysozyme.
  Eur J Biochem, 266, 675-682.
PDB codes: 1c43 1c45 1c46
10350481 K.Takano, Y.Yamagata, M.Kubota, J.Funahashi, S.Fujii, and K.Yutani (1999).
Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants.
  Biochemistry, 38, 6623-6629.
PDB codes: 1b5u 1b5v 1b5w 1b5x 1b5y 1b5z
  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
9788912 Y.Sugita, and A.Kitao (1998).
Dependence of protein stability on the structure of the denatured state: free energy calculations of I56V mutation in human lysozyme.
  Biophys J, 75, 2178-2187.  
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
9265720 B.Lee, and G.Vasmatzis (1997).
Stabilization of protein structures.
  Curr Opin Biotechnol, 8, 423-428.  
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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