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PDBsum entry 206l

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Hydrolase (o-glycosyl) PDB id
206l
Jmol
Contents
Protein chain
162 a.a. *
Ligands
BME
Metals
_CL ×2
Waters ×137
* Residue conservation analysis
PDB id:
206l
Name: Hydrolase (o-glycosyl)
Title: Phage t4 lysozyme
Structure: Lysozyme. Chain: a. Synonym: phage t4 lysozyme. Engineered: yes. Mutation: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665. Cell_line: s2. Gene: t4 lysozyme gene. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.75Å     R-factor:   0.170    
Authors: M.Blaber,B.W.Matthews
Key ref:
M.Blaber et al. (1993). Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. Biochemistry, 32, 11363-11373. PubMed id: 8218201 DOI: 10.1021/bi00093a013
Date:
19-Mar-96     Release date:   17-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00720  (LYS_BPT4) -  Endolysin
Seq:
Struc:
164 a.a.
162 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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     host cell cytoplasm   1 term 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1021/bi00093a013 Biochemistry 32:11363-11373 (1993)
PubMed id: 8218201  
 
 
Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme.
M.Blaber, J.D.Lindstrom, N.Gassner, J.Xu, D.W.Heinz, B.W.Matthews.
 
  ABSTRACT  
 
In order to determine the thermodynamic cost of introducing a polar group within the core of a protein, a series of nine Ala-->Ser and 3 Val-->Thr substitutions was constructed in T4 lysozyme. The sites were all within alpha-helices but ranged from fully solvent-exposed to totally buried. The range of destabilization incurred by the Ala-->Ser substitutions was found to be very similar to that for the Val-->Thr replacements. For the solvent-exposed and partly exposed sites the destabilization was modest (approximately less than 0.5 kcal/mol). For the completely buried sites the destabilization was larger, but variable (approximately 1-3 kcal/mol). Crystal structure determinations showed that the Ala-->Ser mutant structures were, in general, very similar to their wild-type counterparts, even though the replacements introduce a hydroxyl group. This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. The three substituted threonine side chains essentially superimpose on their valine counterparts but display somewhat larger conformational adjustments. The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). Supportive of other studies, the alpha-helix propensity of alanine is seen to be higher than that of serine (delta delta G = 0.46 +/- 0.04 kcal/mol), while threonine and valine are similar in alpha-helix propensity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19384988 B.H.Mooers, W.A.Baase, J.W.Wray, and B.W.Matthews (2009).
Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.
  Protein Sci, 18, 871-880.
PDB codes: 2nzb 2nzk 2nzn 3c7w 3c7y 3c7z 3c80 3c81 3c82 3c83 3c8q 3c8r 3c8s 3cdo 3cdq 3cdr 3cdt 3cdv 3fi5
19525973 J.Gao, D.A.Bosco, E.T.Powers, and J.W.Kelly (2009).
Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins.
  Nat Struct Mol Biol, 16, 684-690.  
  19177365 M.Sagermann, R.R.Chapleau, E.DeLorimier, and M.Lei (2009).
Using affinity chromatography to engineer and characterize pH-dependent protein switches.
  Protein Sci, 18, 217-228.
PDB codes: 3crt 3cru 3d0z
18704951 S.Szep, S.Park, E.T.Boder, G.D.Van Duyne, and J.G.Saven (2009).
Structural coupling between FKBP12 and buried water.
  Proteins, 74, 603-611.
PDB codes: 2ppn 2ppo 2ppp
18373848 M.J.Cuneo, Y.Tian, M.Allert, and H.W.Hellinga (2008).
The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog.
  BMC Struct Biol, 8, 20.
PDB code: 2ioy
17208969 A.Ghosh, K.V.Brinda, and S.Vishveshwara (2007).
Dynamics of lysozyme structure network: probing the process of unfolding.
  Biophys J, 92, 2523-2535.  
16602823 D.A.Kraut, P.A.Sigala, B.Pybus, C.W.Liu, D.Ringe, G.A.Petsko, and D.Herschlag (2006).
Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  PLoS Biol, 4, e99.
PDB codes: 2b32 2pzv
15556980 L.A.Campos, S.Cuesta-López, J.López-Llano, F.Falo, and J.Sancho (2005).
A double-deletion method to quantifying incremental binding energies in proteins from experiment: example of a destabilizing hydrogen bonding pair.
  Biophys J, 88, 1311-1321.  
15937899 S.Park, and J.G.Saven (2005).
Statistical and molecular dynamics studies of buried waters in globular proteins.
  Proteins, 60, 450-463.  
15340171 M.M.He, Z.A.Wood, W.A.Baase, H.Xiao, and B.W.Matthews (2004).
Alanine-scanning mutagenesis of the beta-sheet region of phage T4 lysozyme suggests that tertiary context has a dominant effect on beta-sheet formation.
  Protein Sci, 13, 2716-2724.
PDB codes: 1ssw 1ssy 1t8f 1t8g
15010542 N.Pokala, and T.M.Handel (2004).
Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.
  Protein Sci, 13, 925-936.  
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
14635121 S.Balaji, S.Aruna, and N.Srinivasan (2003).
Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures.
  Proteins, 53, 783-791.  
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.  
12189146 H.S.Mchaourab, E.K.Dodson, and H.A.Koteiche (2002).
Mechanism of chaperone function in small heat shock proteins. Two-mode binding of the excited states of T4 lysozyme mutants by alphaA-crystallin.
  J Biol Chem, 277, 40557-40566.  
11266616 A.Ababou, and J.R.Desjarlais (2001).
Solvation energetics and conformational change in EF-hand proteins.
  Protein Sci, 10, 301-312.  
11298742 A.P.Golovanov, D.Hawkins, I.Barsukov, R.Badii, G.M.Bokoch, L.Y.Lian, and G.C.Roberts (2001).
Structural consequences of site-directed mutagenesis in flexible protein domains: NMR characterization of the L(55,56)S mutant of RhoGDI.
  Eur J Biochem, 268, 2253-2260.  
11316887 J.Xu, W.A.Baase, M.L.Quillin, E.P.Baldwin, and B.W.Matthews (2001).
Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.
  Protein Sci, 10, 1067-1078.
PDB codes: 1g06 1g07 1g0g 1g0j 1g0k 1g0l 1g0m 1g0p 1g0q 1g1v 1g1w 1i6s
  11106173 H.M.Rodriguez, D.M.Vu, and L.M.Gregoret (2000).
Role of a solvent-exposed aromatic cluster in the folding of Escherichia coli CspA.
  Protein Sci, 9, 1993-2000.  
10852713 J.F.Culajay, S.I.Blaber, A.Khurana, and M.Blaber (2000).
Thermodynamic characterization of mutants of human fibroblast growth factor 1 with an increased physiological half-life.
  Biochemistry, 39, 7153-7158.  
  11152136 J.M.Word, R.C.Bateman, B.K.Presley, S.C.Lovell, and D.C.Richardson (2000).
Exploring steric constraints on protein mutations using MAGE/PROBE.
  Protein Sci, 9, 2251-2259.  
11025544 K.T.O'Neil, A.C.Bach, and W.F.DeGrado (2000).
Structural consequences of an amino acid deletion in the B1 domain of protein G.
  Proteins, 41, 323-333.  
  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.  
9565753 B.J.Hillier, H.M.Rodriguez, and L.M.Gregoret (1998).
Coupling protein stability and protein function in Escherichia coli CspA.
  Fold Des, 3, 87-93.  
9761905 D.Wilcock, M.T.Pisabarro, E.López-Hernandez, L.Serrano, and M.Coll (1998).
Structure analysis of two CheY mutants: importance of the hydrogen-bond contribution to protein stability.
  Acta Crystallogr D Biol Crystallogr, 54, 378-385.
PDB codes: 1ab5 1ab6
9442062 M.Alvarez, J.P.Zeelen, V.Mainfroid, F.Rentier-Delrue, J.A.Martial, L.Wyns, R.K.Wierenga, and D.Maes (1998).
Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.
  J Biol Chem, 273, 2199-2206.
PDB codes: 1aw1 1aw2
  9260280 F.Catanzano, G.Graziano, S.Capasso, and G.Barone (1997).
Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A.
  Protein Sci, 6, 1682-1693.  
  8976549 I.R.Vetter, W.A.Baase, D.W.Heinz, J.P.Xiong, S.Snow, and B.W.Matthews (1996).
Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme.
  Protein Sci, 5, 2399-2415.
PDB codes: 209l 210l 211l 212l 213l 214l 215l 218l 219l
8889177 J.K.Myers, and C.N.Pace (1996).
Hydrogen bonding stabilizes globular proteins.
  Biophys J, 71, 2033-2039.  
  8819156 S.M.Habermann, and K.P.Murphy (1996).
Energetics of hydrogen bonding in proteins: a model compound study.
  Protein Sci, 5, 1229-1239.  
7749923 B.W.Matthews (1995).
Can proteins be turned inside-out?
  Nat Struct Biol, 2, 85-86.  
7708669 D.H.Fremont, E.A.Stura, M.Matsumura, P.A.Peterson, and I.A.Wilson (1995).
Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.
  Proc Natl Acad Sci U S A, 92, 2479-2483.
PDB codes: 1vac 1vad
7764905 A.S.el Hawrani, K.M.Moreton, R.B.Sessions, A.R.Clarke, and J.J.Holbrook (1994).
Engineering surface loops of proteins--a preferred strategy for obtaining new enzyme function.
  Trends Biotechnol, 12, 207-211.  
7765172 E.P.Baldwin, and B.W.Matthews (1994).
Core-packing constraints, hydrophobicity and protein design.
  Curr Opin Biotechnol, 5, 396-402.  
  7920248 X.J.Zhang, and B.W.Matthews (1994).
Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme.
  Protein Sci, 3, 1031-1039.
PDB codes: 149l 150l 151l 152l
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.