PDBsum entry 2nth

Hydrolase

PDB id

2nth

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Contents

			Protein chain

					164 a.a. *

			Ligands

					MTN

			Waters ×186

* Residue conservation analysis

PDB id:

2nth

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Name:

Hydrolase

Title:

Structure of spin-labeled t4 lysozyme mutant l118r1

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:

1.80Å

R-factor:

0.183

R-free:

0.212

Authors:

Z.Guo,D.Cascio,K.Hideg,W.L.Hubbell

Key ref:

Z.Guo et al. (2007). Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme. Protein Sci, 16, 1069-1086. PubMed id: 17473014 DOI: 10.1110/ps.062739107

Date:

07-Nov-06

Release date:

12-Jun-07

PROCHECK

	Headers

	References

Protein chain

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.062739107	Protein Sci 16:1069-1086 (2007)
PubMed id: 17473014

Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme.
Z.Guo, D.Cascio, K.Hideg, T.Kálái, W.L.Hubbell.

ABSTRACT

A nitroxide side chain (R1) has been substituted at single sites along a helix-turn-helix motif in T4 lysozyme (residues 114-135). Together with previously published data, the new sites reported complete a continuous scan through the motif. Mutants with R1 at sites 115 and 118 were selected for crystallographic analysis to identify the structural origins of the corresponding two-component EPR spectra. At 115, R1 is shown to occupy two rotamers in the room temperature crystal structure, one of which has not been previously reported. The two components in the EPR spectrum apparently arise from differential interactions of the two rotamers with the surrounding structure, the most important of which is a hydrophobic interaction of the nitroxide ring. Interestingly, the crystal structure at 100 K reveals a single rotamer, emphasizing the possibility of rotamer selection in low-temperature crystal structures. Residue 118 is at a solvent-inaccessible site in the protein core, and the structure of 118R1, the first reported for the R1 side chain at a buried site, reveals how the side chain is accommodated in an overpacked core.

Selected figure(s)



	Figure 8. Figure 8. The effect of dioxane and mutation of nearest-neighbor residues

Figure was 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.

21271275

T.Gruene, M.K.Cho, I.Karyagina, H.Y.Kim, C.Grosse, K.Giller, M.Zweckstetter, and S.Becker (2011).
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.

J Biomol NMR, 49, 111-119.

PDB codes:

2xi8 2xiu 2xj3

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.

20014029

R.H.Flores Jiménez, M.A.Do Cao, M.Kim, and D.S.Cafiso (2010).
Osmolytes modulate conformational exchange in solvent-exposed regions of membrane proteins.

Protein Sci, 19, 269-278.

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.

19124026

D.M.Hatters, J.C.Voss, M.S.Budamagunta, Y.N.Newhouse, and K.H.Weisgraber (2009).
Insight on the molecular envelope of lipid-bound apolipoprotein E from electron paramagnetic resonance spectroscopy.

J Mol Biol, 386, 261-271.

19191603

D.Sezer, J.H.Freed, and B.Roux (2009).
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations.

J Am Chem Soc, 131, 2597-2605.

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.

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.

18447510

D.Sezer, J.H.Freed, and B.Roux (2008).
Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories.

J Chem Phys, 128, 165106.

18412413

D.Sezer, J.H.Freed, and B.Roux (2008).
Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix.

J Phys Chem B, 112, 5755-5767.

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.

18586842

Q.Xu, M.Kim, K.W.Ho, P.Lachowicz, G.E.Fanucci, and D.S.Cafiso (2008).
Membrane hydrocarbon thickness modulates the dynamics of a membrane transport protein.

Biophys J, 95, 2849-2858.

18234808

S.C.DeSensi, D.P.Rangel, A.H.Beth, T.P.Lybrand, and E.J.Hustedt (2008).
Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.

Biophys J, 94, 3798-3809.

18096642

Z.Guo, D.Cascio, K.Hideg, and W.L.Hubbell (2008).
Structural determinants of nitroxide motion in spin-labeled proteins: solvent-exposed sites in helix B of T4 lysozyme.

Protein Sci, 17, 228-239.

PDB codes:

2q9d 2q9e

17925435

I.Smirnova, V.Kasho, J.Y.Choe, C.Altenbach, W.L.Hubbell, and H.R.Kaback (2007).
Sugar binding induces an outward facing conformation of LacY.

Proc Natl Acad Sci U S A, 104, 16504-16509.

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.