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PDBsum entry 1b5y
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protein metals links
Hydrolase PDB id
1b5y

 

 

 

 

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Contents
Protein chain
130 a.a. *
Metals
_NA
Waters ×168
* Residue conservation analysis
PDB id:
1b5y
Name: Hydrolase
Title: Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and x-ray analysis of six ser->ala mutants
Structure: Protein (lysozyme). Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Strain: ah22r-. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
2.20Å     R-factor:   0.148    
Authors: K.Takano,Y.Yamagata,M.Kubota,J.Funahashi,S.Fujii,K.Yutani
Key ref:
K.Takano et al. (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. PubMed id: 10350481 DOI: 10.1021/bi9901228
Date:
11-Jan-99     Release date:   20-Jan-99    
PROCHECK
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 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/bi9901228 Biochemistry 38:6623-6629 (1999)
PubMed id: 10350481  
 
 
Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants.
K.Takano, Y.Yamagata, M.Kubota, J.Funahashi, S.Fujii, K.Yutani.
 
  ABSTRACT  
 
To further examine the contribution of hydrogen bonds to the conformational stability of the human lysozyme, six Ser to Ala mutants were constructed. The thermodynamic parameters for denaturation of these six Ser mutant proteins were investigated by differential scanning calorimetry (DSC), and the crystal structures were determined by X-ray analysis. The denaturation Gibbs energy (DeltaG) of the Ser mutant proteins was changed from 2.0 to -5.7 kJ/mol, compared to that of the wild-type protein. With an analysis in which some factors that affected the stability due to mutation were considered, the contribution of hydrogen bonds to the stability (Delta DeltaGHB) was extracted on the basis of the structures of the mutant proteins. The results showed that hydrogen bonds between protein atoms and between a protein atom and a water bound with the protein molecule favorably contribute to the protein stability. The net contribution of one intramolecular hydrogen bond to protein stability (DeltaGHB) was 8.9 +/- 2.6 kJ/mol on average. However, the contribution to the protein stability of hydrogen bonds between a protein atom and a bound water molecule was smaller than that for a bond between protein atoms.
 

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.  
17631502 B.S.Hong, G.Senisterra, W.M.Rabeh, M.Vedadi, R.Leonardi, Y.M.Zhang, C.O.Rock, S.Jackowski, and H.W.Park (2007).
Crystal structures of human pantothenate kinases. Insights into allosteric regulation and mutations linked to a neurodegeneration disorder.
  J Biol Chem, 282, 27984-27993.
PDB codes: 2i7n 2i7p
17591767 E.B.Askew, R.T.Gampe, T.B.Stanley, J.L.Faggart, and E.M.Wilson (2007).
Modulation of androgen receptor activation function 2 by testosterone and dihydrotestosterone.
  J Biol Chem, 282, 25801-25816.
PDB codes: 2q7i 2q7j 2q7k 2q7l
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.  
17242738 Z.Li, and T.Lazaridis (2007).
Water at biomolecular binding interfaces.
  Phys Chem Chem Phys, 9, 573-581.  
16386393 A.Badkar, P.Yohannes, and A.Banga (2006).
Application of TZERO calibrated modulated temperature differential scanning calorimetry to characterize model protein formulations.
  Int J Pharm, 309, 146-156.  
16353166 D.Schell, J.Tsai, J.M.Scholtz, and C.N.Pace (2006).
Hydrogen bonding increases packing density in the protein interior.
  Proteins, 63, 278-282.  
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.  
16154093 D.B.Huang, D.Vu, and G.Ghosh (2005).
NF-kappaB RelB forms an intertwined homodimer.
  Structure, 13, 1365-1373.
PDB codes: 1zk9 1zka
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.  
12799387 K.Takano, J.M.Scholtz, J.C.Sacchettini, and C.N.Pace (2003).
The contribution of polar group burial to protein stability is strongly context-dependent.
  J Biol Chem, 278, 31790-31795.
PDB codes: 1uci 1ucj 1uck 1ucl
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
11751325 P.R.Pokkuluri, R.Raffen, L.Dieckman, C.Boogaard, F.J.Stevens, and M.Schiffer (2002).
Increasing protein stability by polar surface residues: domain-wide consequences of interactions within a loop.
  Biophys J, 82, 391-398.
PDB code: 1eeq
11344322 D.P.Goldenberg, R.E.Koehn, D.E.Gilbert, and G.Wagner (2001).
Solution structure and backbone dynamics of an omega-conotoxin precursor.
  Protein Sci, 10, 538-550.
PDB code: 1feo
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
11266603 M.Zavodszky, C.W.Chen, J.K.Huang, M.Zolkiewski, L.Wen, and R.Krishnamoorthi (2001).
Disulfide bond effects on protein stability: designed variants of Cucurbita maxima trypsin inhibitor-V.
  Protein Sci, 10, 149-160.  
11567098 R.Ragone (2001).
Hydrogen-bonding classes in proteins and their contribution to the unfolding reaction.
  Protein Sci, 10, 2075-2082.  
11169391 Z.W.Cao, and Y.Z.Chen (2001).
Hydrogen-bond disruption probability in proteins by a modified self-consistent harmonic approach.
  Biopolymers, 58, 319-328.  
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
  10548065 Q.Wang, A.M.Buckle, N.W.Foster, C.M.Johnson, and A.R.Fersht (1999).
Design of highly stable functional GroEL minichaperones.
  Protein Sci, 8, 2186-2193.  
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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