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PDBsum entry 1ckh
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Hydrolase PDB id
1ckh

 

 

 

 

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Contents
Protein chain
130 a.a. *
Waters ×238
* Residue conservation analysis
PDB id:
1ckh
Name: Hydrolase
Title: T70v mutant human lysozyme
Structure: Protein (lysozyme). Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Other_details: synthetic gene
Resolution:
2.00Å     R-factor:   0.183    
Authors: K.Takano,Y.Yamagata,J.Funahashi,K.Yutani
Key ref:
K.Takano et al. (1999). Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,). Biochemistry, 38, 12698-12708. PubMed id: 10504240 DOI: 10.1021/bi9910169
Date:
22-Apr-99     Release date:   30-Apr-99    
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/bi9910169 Biochemistry 38:12698-12708 (1999)
PubMed id: 10504240  
 
 
Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,).
K.Takano, Y.Yamagata, J.Funahashi, Y.Hioki, S.Kuramitsu, K.Yutani.
 
  ABSTRACT  
 
In globular proteins, there are intermolecular hydrogen bonds between protein and water molecules, and between water molecules, which are bound with the proteins, in addition to intramolecular hydrogen bonds. To estimate the contribution of these hydrogen bonds to the conformational stability of a protein, the thermodynamic parameters for denaturation and the crystal structures of five Thr to Val and five Thr to Ala mutant human lysozymes were determined. The denaturation Gibbs energy (DeltaG) of Thr to Val and Thr to Ala mutant proteins was changed from 4.0 to -5.6 kJ/mol and from 1.6 to -6.3 kJ/mol, respectively, compared with that of the wild-type protein. The contribution of hydrogen bonds to the stability (DeltaDeltaG(HB)) of the Thr and other mutant human lysozymes previously reported was extracted from the observed stability changes (DeltaDeltaG) with correction for changes in hydrophobicity and side chain conformational entropy between the wild-type and mutant structures. The estimation of the DeltaDeltaG(HB) values of all mutant proteins after removal of hydrogen bonds, including protein-water hydrogen bonds, indicates a favorable contribution of the intra- and intermolecular hydrogen bonds to the protein stability. The net contribution of an intramolecular hydrogen bond (DeltaG(HB[pp])), an intermolecular one between protein and ordered water molecules (DeltaG(HB[pw])), and an intermolecular one between ordered water molecules (DeltaG(HB[ww])) could be estimated to be 8. 5, 5.2, and 5.0 kJ/mol, respectively, for a 3 A long hydrogen bond. This result shows the different contributions to protein stability of intra- and intermolecular hydrogen bonds. The entropic cost due to the introduction of a water molecule (DeltaG(H)()2(O)) could be also estimated to be about 8 kJ/mol.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21075614 J.U.Bowie (2011).
Membrane protein folding: how important are hydrogen bonds?
  Curr Opin Struct Biol, 21, 42-49.  
20937603 S.Ayuso-Tejedor, O.Abián, and J.Sancho (2011).
Underexposed polar residues and protein stabilization.
  Protein Eng Des Sel, 24, 171-177.  
19864691 T.Nakamura, S.Meshitsuka, S.Kitagawa, N.Abe, J.Yamada, T.Ishino, H.Nakano, T.Tsuzuki, T.Doi, Y.Kobayashi, S.Fujii, M.Sekiguchi, and Y.Yamagata (2010).
Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.
  J Biol Chem, 285, 444-452.
PDB codes: 3a6s 3a6t 3a6u 3a6v
18391411 K.Shimizu, C.Kuroishi, M.Sugahara, and N.Kunishima (2008).
Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.
  Acta Crystallogr D Biol Crystallogr, 64, 444-453.
PDB codes: 1wn2 2d3k
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.  
16597831 L.A.Clark, P.A.Boriack-Sjodin, J.Eldredge, C.Fitch, B.Friedman, K.J.Hanf, M.Jarpe, S.F.Liparoto, Y.Li, A.Lugovskoy, S.Miller, M.Rushe, W.Sherman, K.Simon, and H.Van Vlijmen (2006).
Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design.
  Protein Sci, 15, 949-960.
PDB code: 2b2x
16239727 M.Sugahara, N.Ohshima, Y.Ukita, M.Sugahara, and N.Kunishima (2005).
Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.
  Acta Crystallogr D Biol Crystallogr, 61, 1500-1507.
PDB codes: 1j3b 1xkv
15937286 P.J.Fleming, and G.D.Rose (2005).
Do all backbone polar groups in proteins form hydrogen bonds?
  Protein Sci, 14, 1911-1917.  
15608125 S.D.Sharrow, K.A.Edmonds, M.A.Goodman, M.V.Novotny, and M.J.Stone (2005).
Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex.
  Protein Sci, 14, 249-256.  
14684898 H.Takahashi, E.Inagaki, Y.Fujimoto, C.Kuroishi, Y.Nodake, Y.Nakamura, F.Arisaka, K.Yutani, S.Kuramitsu, S.Yokoyama, M.Yamamoto, M.Miyano, and T.H.Tahirov (2004).
Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 60, 97.
PDB code: 1od6
15388928 N.K.Lokanath, I.Shiromizu, N.Ohshima, Y.Nodake, M.Sugahara, S.Yokoyama, S.Kuramitsu, M.Miyano, and N.Kunishima (2004).
Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.
  Acta Crystallogr D Biol Crystallogr, 60, 1816-1823.
PDB codes: 1j2w 1ub3
15206928 Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, and K.Yutani (2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
  Eur J Biochem, 271, 2624-2635.
PDB code: 1v8z
12709420 G.Esposito, J.Garcia, P.Mangione, S.Giorgetti, A.Corazza, P.Viglino, F.Chiti, A.Andreola, P.Dumy, D.Booth, P.N.Hawkins, and V.Bellotti (2003).
Structural and folding dynamic properties of the T70N variant of human lysozyme.
  J Biol Chem, 278, 25910-25918.  
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.  
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
12214315 J.Higo, and M.Nakasako (2002).
Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole.
  J Comput Chem, 23, 1323-1336.
PDB code: 1jwr
11121116 K.Takano, J.Funahashi, and K.Yutani (2001).
The stability and folding process of amyloidogenic mutant human lysozymes.
  Eur J Biochem, 268, 155-159.  
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.  
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
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
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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