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Hydrolase(o-glycosyl) PDB id
143l
Jmol
Contents
Protein chain
162 a.a. *
Ligands
BME-BME
Metals
_CL ×2
Waters ×106
* Residue conservation analysis
PDB id:
143l
Name: Hydrolase(o-glycosyl)
Title: Role of backbone flexibility in the accommodation of variants that repack the core of t4 lysozyme
Structure: T4 lysozyme. Chain: a. Engineered: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.158    
Authors: E.Baldwin,B.W.Matthews
Key ref: E.P.Baldwin et al. (1993). The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science, 262, 1715-1718. PubMed id: 8259514 DOI: 10.1126/science.8259514
Date:
15-Oct-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00720  (LYS_BPT4) -  Lysozyme
Seq:
Struc: 		164 a.a.
162 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 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!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1126/science.8259514 Science 262:1715-1718 (1993)
PubMed id: 8259514  
 
 
The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme.
E.P.Baldwin, O.Hajiseyedjavadi, W.A.Baase, B.W.Matthews.
 
  ABSTRACT  
 
To understand better how the packing of side chains within the core influences protein structure and stability, the crystal structures were determined for eight variants of T4 lysozyme, each of which contains three to five substitutions at adjacent interior sites. Concerted main-chain and side-chain displacements, with movements of helical segments as large as 0.8 angstrom, were observed. In contrast, the angular conformations of the mutated side chains tended to remain unchanged, with torsion angles within 20 degrees of those in the wild-type structure. These observations suggest that not only the rotation of side chains but also movements of the main chain must be considered in the evaluation of which amino acid sequences are compatible with a given protein fold.
 

Literature references that cite this PDB file's key reference

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PDB codes: 3crt 3cru 3d0z
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Structural determinants of nitroxide motion in spin-labeled proteins: tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme.
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PDB codes: 2igc 2ntg 2nth 2ou8 2ou9
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PDB codes: 1fcl 1fd6
11714927 S.R.Brych, S.I.Blaber, T.M.Logan, and M.Blaber (2001).
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PDB codes: 1jqz 1jt3 1jt4 1jt5 1jt7 1jtc
11592132 S.V.Taylor, P.Kast, and D.Hilvert (2001).
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Rotamer strain as a determinant of protein structural specificity.
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PDB code: 1c3t
  10210193 M.A.Ceruso, A.Amadei, and A.Di Nola (1999).
Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues.
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10450085 M.A.Ceruso, A.Grottesi, and A.Di Nola (1999).
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Mutually compensatory mutations during evolution of the tetramerization domain of tumor suppressor p53 lead to impaired hetero-oligomerization.
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10611303 S.J.Lahr, A.Broadwater, C.W.Carter, M.L.Collier, L.Hensley, J.C.Waldner, G.J.Pielak, and M.H.Edgell (1999).
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The de novo design of a rubredoxin-like Fe site.
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Hydrophobic core packing and protein design.
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Opioid receptor three-dimensional structures from distance geometry calculations with hydrogen bonding constraints.
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Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization.
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Hydrophobic side-chain size is a determinant of the three-dimensional structure of the p53 oligomerization domain.
  EMBO J, 16, 6230-6236.
PDB code: 1a1u
8672470 H.S.Mchaourab, M.A.Lietzow, K.Hideg, and W.L.Hubbell (1996).
Motion of spin-labeled side chains in T4 lysozyme. Correlation with protein structure and dynamics.
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8696970 M.H.Cordes, A.R.Davidson, and R.T.Sauer (1996).
Sequence space, folding and protein design.
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8973214 M.J.Rodríguez-Marañón, F.Qiu, R.E.Stark, S.P.White, X.Zhang, S.I.Foundling, V.Rodríguez, C.L.Schilling, R.A.Bunce, and M.Rivera (1996).
13C NMR spectroscopic and X-ray crystallographic study of the role played by mitochondrial cytochrome b5 heme propionates in the electrostatic binding to cytochrome c.
  Biochemistry, 35, 16378-16390.
PDB code: 1b5m
  8844848 M.Munson, S.Balasubramanian, K.G.Fleming, A.D.Nagi, R.O'Brien, J.M.Sturtevant, and L.Regan (1996).
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8901549 N.C.Gassner, W.A.Baase, and B.W.Matthews (1996).
A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme.
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7749923 B.W.Matthews (1995).
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Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase.
  Nat Struct Biol, 2, 244-249.
PDB code: 1hvs
  8535237 J.R.Desjarlais, and T.M.Handel (1995).
De novo design of the hydrophobic cores of proteins.
  Protein Sci, 4, 2006-2018.  
  7613459 K.A.Dill, S.Bromberg, K.Yue, K.M.Fiebig, D.P.Yee, P.D.Thomas, and H.S.Chan (1995).
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  Protein Sci, 4, 561-602.  
7758464 K.L.Britton, P.J.Baker, K.M.Borges, P.C.Engel, A.Pasquo, D.W.Rice, F.T.Robb, R.Scandurra, T.J.Stillman, and K.S.Yip (1995).
Insights into thermal stability from a comparison of the glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis.
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7479696 N.Foloppe, M.Ferrand, J.Breton, and J.C.Smith (1995).
Structural model of the photosynthetic reaction center of Rhodobacter capsulatus.
  Proteins, 22, 226-244.
PDB code: 1clt
7667303 P.B.Harbury, B.Tidor, and P.S.Kim (1995).
Repacking protein cores with backbone freedom: structure prediction for coiled coils.
  Proc Natl Acad Sci U S A, 92, 8408-8412.  
  7663353 P.B.Laub, S.Khorasanizadeh, and H.Roder (1995).
Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints.
  Protein Sci, 4, 973-982.  
8618841 S.Choe, C.F.Stevens, and J.M.Sullivan (1995).
Three distinct structural environments of a transmembrane domain in the inwardly rectifying potassium channel ROMK1 defined by perturbation.
  Proc Natl Acad Sci U S A, 92, 12046-12049.  
  7579646 S.J.Hubbard, and P.Argos (1995).
Evidence on close packing and cavities in proteins.
  Curr Opin Biotechnol, 6, 375-381.  
  7765167 A.C.May, and T.L.Blundell (1994).
Automated comparative modelling of protein structures.
  Curr Opin Biotechnol, 5, 355-360.  
  7765172 E.P.Baldwin, and B.W.Matthews (1994).
Core-packing constraints, hydrophobicity and protein design.
  Curr Opin Biotechnol, 5, 396-402.  
  7535612 M.Munson, R.O'Brien, J.M.Sturtevant, and L.Regan (1994).
Redesigning the hydrophobic core of a four-helix-bundle protein.
  Protein Sci, 3, 2015-2022.  
  7920265 S.Bromberg, and K.A.Dill (1994).
Side-chain entropy and packing in proteins.
  Protein Sci, 3, 997.  
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.