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PDBsum entry 2q9d
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Hydrolase PDB id
2q9d

 

 

 

 

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Contents
Protein chain
164 a.a. *
Ligands
MTN
BME
Waters ×230
* Residue conservation analysis
PDB id:
2q9d
Name: Hydrolase
Title: Structure of spin-labeled t4 lysozyme mutant a41r1
Structure: Lysozyme. Chain: a. Synonym: lysis protein, muramidase, endolysin. Engineered: yes. Mutation: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665. Gene: e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.40Å     R-factor:   0.152     R-free:   0.202
Authors: Z.Guo,D.Cascio,K.Hideg,W.L.Hubbell
Key ref:
Z.Guo et al. (2008). Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozyme. Protein Sci, 17, 228-239. PubMed id: 18096642 DOI: 10.1110/ps.073174008
Date:
12-Jun-07     Release date:   26-Jun-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4
Seq:
Struc: 		164 a.a.
164 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.

 

 
DOI no: 10.1110/ps.073174008 Protein Sci 17:228-239 (2008)
PubMed id: 18096642  
 
 
Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozyme.
Z.Guo, D.Cascio, K.Hideg, W.L.Hubbell.
 
  ABSTRACT  
 
Site-directed spin labeling provides a means for exploring structure and dynamics in proteins. To interpret the complex EPR spectra that often arise, it is necessary to characterize the rotamers of the spin-labeled side chain and the interactions they make with the local environment in proteins of known structure. For this purpose, crystal structures have been determined for T4 lysozyme bearing a nitroxide side chain (R1) at the solvent-exposed helical sites 41 and 44 in the B helix. These sites are of particular interest in that the corresponding EPR spectra reveal two dynamic states of R1, one of which is relatively immobilized suggesting interactions of the nitroxide with the environment. The crystal structures together with the effect of mutagenesis of nearest neighbors on the motion of R1 suggest intrahelical interactions of 41R1 with the i + 4 residue and of 44R1 with the i + 1 residue. Such interactions appear to be specific to particular rotamers of the R1 side chain.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the nitroxide side chain R1 showing designation of the various atoms and side-chain dihedral angles ( ). [5] is defined by S[ ]–C[ ]–C[3]–C[4] as in Tombolato et al. (2006). 		Figure 3.
Figure 3. Structure of 41R1. (A) Electron density superimposed on a stick model of 41R1. The 2F [o]–F [c] map is contoured at 1.3 . (B) Distance of the S[ ]atom of the disulfide group from the H atom modeled on 41C[ ]. (C) Distances of atoms in the nitroxide ring from nearest neighbors in the lattice. A symmetry-related molecule is colored cyan, and residues belonging to this molecule are indicated with a prime ('). (D) Space-filling model of 41R1 and neighboring groups.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2008, 17, 228-239) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21162593 D.T.Warshaviak, L.Serbulea, K.N.Houk, and W.L.Hubbell (2011).
Conformational analysis of a nitroxide side chain in an α-helix with density functional theory.
  J Phys Chem B, 115, 397-405.  
21205903 J.McCoy, and W.L.Hubbell (2011).
High-pressure EPR reveals conformational equilibria and volumetric properties of spin-labeled proteins.
  Proc Natl Acad Sci U S A, 108, 1331-1336.  
21279205 V.S.Oganesyan (2011).
A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein.
  Phys Chem Chem Phys, 13, 4724-4737.  
21116569 Y.Polyhach, E.Bordignon, and G.Jeschke (2011).
Rotamer libraries of spin labelled cysteines for protein studies.
  Phys Chem Chem Phys, 13, 2356-2366.  
  20157634 M.D.Bridges, K.Hideg, and W.L.Hubbell (2010).
Resolving Conformational and Rotameric Exchange in Spin-Labeled Proteins Using Saturation Recovery EPR.
  Appl Magn Reson, 37, 363.  
20830439 T.C.Sung, and Y.W.Chiang (2010).
Identification of complex dynamic modes on prion protein peptides using multifrequency ESR with mesoporous materials.
  Phys Chem Chem Phys, 12, 13117-13125.  
20361789 Z.Zhang, M.R.Fleissner, D.S.Tipikin, Z.Liang, J.K.Moscicki, K.A.Earle, W.L.Hubbell, and J.H.Freed (2010).
Multifrequency electron spin resonance study of the dynamics of spin labeled T4 lysozyme.
  J Phys Chem B, 114, 5503-5521.  
19919160 B.Endeward, J.A.Butterwick, R.MacKinnon, and T.F.Prisner (2009).
Pulsed electron-electron double-resonance determination of spin-label distances and orientations on the tetrameric potassium ion channel KcsA.
  J Am Chem Soc, 131, 15246-15250.  
19585559 C.J.López, M.R.Fleissner, Z.Guo, A.K.Kusnetzow, and W.L.Hubbell (2009).
Osmolyte perturbation reveals conformational equilibria in spin-labeled proteins.
  Protein Sci, 18, 1637-1652.  
19501597 D.Z.Herrick, W.Kuo, H.Huang, C.D.Schwieters, J.F.Ellena, and D.S.Cafiso (2009).
Solution and membrane-bound conformations of the tandem C2A and C2B domains of synaptotagmin 1: Evidence for bilayer bridging.
  J Mol Biol, 390, 913-923.  
19384990 M.R.Fleissner, D.Cascio, and W.L.Hubbell (2009).
Structural origin of weakly ordered nitroxide motion in spin-labeled proteins.
  Protein Sci, 18, 893-908.
PDB codes: 1zyt 2cuu 3g3v 3g3w 3g3x
19995976 M.R.Fleissner, E.M.Brustad, T.Kálai, C.Altenbach, D.Cascio, F.B.Peters, K.Hideg, P.G.Schultz, and W.L.Hubbell (2009).
Site-directed spin labeling of a genetically encoded unnatural amino acid.
  Proc Natl Acad Sci U S A, 106, 21637-21642.
PDB code: 3hwl
19368558 P.O.Heidarsson, S.T.Sigurdsson, and B.Asgeirsson (2009).
Structural features and dynamics of a cold-adapted alkaline phosphatase studied by EPR spectroscopy.
  FEBS J, 276, 2725-2735.  
19302798 W.Kuo, D.Z.Herrick, J.F.Ellena, and D.S.Cafiso (2009).
The calcium-dependent and calcium-independent membrane binding of synaptotagmin 1: two modes of C2B binding.
  J Mol Biol, 387, 284-294.  
18490656 C.Altenbach, A.K.Kusnetzow, O.P.Ernst, K.P.Hofmann, and W.L.Hubbell (2008).
High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation.
  Proc Natl Acad Sci U S A, 105, 7439-7444.  
18783249 C.Antoniou, V.Q.Lam, and L.W.Fung (2008).
Conformational changes at the tetramerization site of erythroid alpha-spectrin upon binding beta-spectrin: a spin label EPR study.
  Biochemistry, 47, 10765-10772.  
18956883 H.Huang, and D.S.Cafiso (2008).
Conformation and membrane position of the region linking the two C2 domains in synaptotagmin 1 by site-directed spin labeling.
  Biochemistry, 47, 12380-12388.  
18697747 M.Doebber, E.Bordignon, J.P.Klare, J.Holterhues, S.Martell, N.Mennes, L.Li, M.Engelhard, and H.J.Steinhoff (2008).
Salt-driven equilibrium between two conformations in the HAMP domain from Natronomonas pharaonis: the language of signal transfer?
  J Biol Chem, 283, 28691-28701.  
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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