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PDBsum entry 1gxv
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Hydrolase PDB id
1gxv

 

 

 

 

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Contents
Protein chain
129 a.a. *
Waters ×15
* Residue conservation analysis
PDB id:
1gxv
Name: Hydrolase
Title: Solution structure of lysozyme at low and high pressure
Structure: LysozymE C. Chain: 2. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d 4. Ec: 3.2.1.17
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: egg-white
NMR struc: 1 models
Authors: M.Refaee,K.Akasaka,M.Williamson
Key ref:
M.Refaee et al. (2003). Pressure-dependent changes in the solution structure of hen egg-white lysozyme. J Mol Biol, 327, 857-865. PubMed id: 12654268 DOI: 10.1016/S0022-2836(03)00209-2
Date:
12-Apr-02     Release date:   27-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus
Seq:
Struc: 		147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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: 10.1016/S0022-2836(03)00209-2 J Mol Biol 327:857-865 (2003)
PubMed id: 12654268  
 
 
Pressure-dependent changes in the solution structure of hen egg-white lysozyme.
M.Refaee, T.Tezuka, K.Akasaka, M.P.Williamson.
 
  ABSTRACT  
 
The "rules" governing protein structure and stability are still poorly understood. Important clues have come from proteins that operate under extreme conditions, because these clarify the physical constraints on proteins. One obvious extreme is pressure, but so far little is known of the behavior of proteins under pressure, largely for technical reasons. We have therefore developed new methodology for calculating structure change in solution with pressure, using NMR chemical shift changes, and we report the change in structure of lysozyme on going from 30 bar to 2000 bar, this being the first solution structure of a globular protein under pressure. The alpha-helical domain is compressed by approximately 1%, due to tighter packing between helices. The interdomain region is also compressed. By contrast, the beta-sheet domain displays very little overall compression, but undergoes more structural distortion than the alpha-domain. The largest volume changes tend to occur close to hydrated cavities. Because isothermal compressibility is related to volume fluctuation, this suggests that buried water molecules play an important role in conformational fluctuation at normal pressures, and are implicated as the nucleation sites for structural changes leading to pressure denaturation or channel opening.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Test for motion about hinge axis. Histogram of rotation (change in th, high pressure -low pressure) around the 38-97 axis, for all heavy atoms. A unimodal distribution indicates no hinge bending. 		Figure 5.
Figure 5. Distance from C^a atom to nearest buried water molecule, plotted against absolute change in amino acid Voronoi volume,[38.] for all completely buried atoms. Only residues with volume change greater than 2 Å3 are shown. Compression is shown in red, and expansion in black.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 857-865) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21275639 M.D.Collins, C.U.Kim, and S.M.Gruner (2011).
High-pressure protein crystallography and NMR to explore protein conformations.
  Annu Rev Biophys, 40, 81-98.  
21170380 C.B.Fowler, I.E.Chesnick, C.D.Moore, T.J.O'Leary, and J.T.Mason (2010).
Elevated pressure improves the extraction and identification of proteins recovered from formalin-fixed, paraffin-embedded tissue surrogates.
  PLoS One, 5, e14253.  
20409483 J.R.Grigera, and A.N.McCarthy (2010).
The behavior of the hydrophobic effect under pressure and protein denaturation.
  Biophys J, 98, 1626-1631.  
19751677 B.Barstow, N.Ando, C.U.Kim, and S.M.Gruner (2009).
Coupling of pressure-induced structural shifts to spectral changes in a yellow fluorescent protein.
  Biophys J, 97, 1719-1727.  
19720037 D.J.Wilton, R.Kitahara, K.Akasaka, M.J.Pandya, and M.P.Williamson (2009).
Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations.
  Biophys J, 97, 1482-1490.
PDB codes: 2kf3 2kf4 2kf5 2kf6
19308328 D.J.Wilton, R.Kitahara, K.Akasaka, and M.P.Williamson (2009).
Pressure-dependent 13C chemical shifts in proteins: origins and applications.
  J Biomol NMR, 44, 25-33.  
19034695 J.F.Treml, Y.Hao, J.E.Stadanlick, and M.P.Cancro (2009).
The BLyS family: toward a molecular understanding of B cell homeostasis.
  Cell Biochem Biophys, 53, 1.  
19570795 M.G.Ortore, F.Spinozzi, P.Mariani, A.Paciaroni, L.R.Barbosa, H.Amenitsch, M.Steinhart, J.Ollivier, and D.Russo (2009).
Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution.
  J R Soc Interface, 6, S619-S634.  
19416064 R.Fourme, E.Girard, R.Kahn, A.C.Dhaussy, and I.Ascone (2009).
Advances in high-pressure biophysics: status and prospects of macromolecular crystallography.
  Annu Rev Biophys, 38, 153-171.  
18768811 B.Barstow, N.Ando, C.U.Kim, and S.M.Gruner (2008).
Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.
  Proc Natl Acad Sci U S A, 105, 13362-13366.
PDB codes: 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu
18158558 C.B.Fowler, R.E.Cunningham, T.J.Waybright, J.Blonder, T.D.Veenstra, T.J.O'Leary, and J.T.Mason (2008).
Elevated hydrostatic pressure promotes protein recovery from formalin-fixed, paraffin-embedded tissue surrogates.
  Lab Invest, 88, 185-195.  
18515837 D.J.Wilton, M.Ghosh, K.V.Chary, K.Akasaka, and M.P.Williamson (2008).
Structural change in a B-DNA helix with hydrostatic pressure.
  Nucleic Acids Res, 36, 4032-4037.
PDB codes: 2vah 2vai
18076052 D.J.Wilton, R.B.Tunnicliffe, Y.O.Kamatari, K.Akasaka, and M.P.Williamson (2008).
Pressure-induced changes in the solution structure of the GB1 domain of protein G.
  Proteins, 71, 1432-1440.
PDB codes: 2j52 2j53
18282073 V.Calandrini, and G.R.Kneller (2008).
Influence of pressure on the slow and fast fractional relaxation dynamics in lysozyme: a simulation study.
  J Chem Phys, 128, 065102.  
18163743 J.Kohlbrecher, A.Bollhalder, R.Vavrin, and G.Meier (2007).
A high pressure cell for small angle neutron scattering up to 500 MPa in combination with light scattering to investigate liquid samples.
  Rev Sci Instrum, 78, 125101.  
17956984 L.Meinhold, J.C.Smith, A.Kitao, and A.H.Zewail (2007).
Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.
  Proc Natl Acad Sci U S A, 104, 17261-17265.  
17292912 M.D.Collins, M.L.Quillin, G.Hummer, B.W.Matthews, and S.M.Gruner (2007).
Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.
  J Mol Biol, 367, 752-763.
PDB codes: 2b6t 2oe7 2oe9 2oea
17660257 T.Imai, S.Ohyama, A.Kovalenko, and F.Hirata (2007).
Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin.
  Protein Sci, 16, 1927-1933.  
16917942 D.Trzesniak, R.D.Lins, and W.F.van Gunsteren (2006).
Protein under pressure: molecular dynamics simulation of the arc repressor.
  Proteins, 65, 136-144.  
16510977 G.R.Kneller, and P.Calligari (2006).
Efficient characterization of protein secondary structure in terms of screw motions.
  Acta Crystallogr D Biol Crystallogr, 62, 302-311.  
17038664 P.Cioni (2006).
Role of protein cavities on unfolding volume change and on internal dynamics under pressure.
  Biophys J, 91, 3390-3396.  
16848614 Y.Harano, and M.Kinoshita (2006).
Crucial importance of translational entropy of water in pressure denaturation of proteins.
  J Chem Phys, 125, 24910.  
15983410 C.U.Kim, R.Kapfer, and S.M.Gruner (2005).
High-pressure cooling of protein crystals without cryoprotectants.
  Acta Crystallogr D Biol Crystallogr, 61, 881-890.  
15731378 E.Girard, R.Kahn, M.Mezouar, A.C.Dhaussy, T.Lin, J.E.Johnson, and R.Fourme (2005).
The first crystal structure of a macromolecular assembly under high pressure: CpMV at 330 MPa.
  Biophys J, 88, 3562-3571.  
16485975 L.Meinhold, and J.C.Smith (2005).
Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation.
  Phys Rev E Stat Nonlin Soft Matter Phys, 72, 061908.  
12930996 M.P.Williamson, K.Akasaka, and M.Refaee (2003).
The solution structure of bovine pancreatic trypsin inhibitor at high pressure.
  Protein Sci, 12, 1971-1979.
PDB codes: 1oa5 1oa6
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.

 

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