4TUN | pdb_00004tun

Crystal structure of Chicken egg white lysozyme adduct with Organophosphorus pesticide Monochrotophos

PDB DOI: https://doi.org/10.2210/pdb4TUN/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2014-06-24 Released: 2014-07-09
Deposition Author(s): Amaraneni, S.R., Kumar, S., Samudrala, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.229 (Depositor), 0.240 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Biophysical aspects of lysozyme adduct with monocrotophos.

Amaraneni, S.R., Kumar, S., Gourinath, S.

(2014) Anal Bioanal Chem 406: 5477-5485

PubMed: 24969463 Search on PubMed
DOI: https://doi.org/10.1007/s00216-014-7953-y
Primary Citation Related Structures:
4TUN

PubMed Abstract:
The present study on in vitro formation and characterization of lysozyme adduct with monocrotophos (MP) evaluates the potential of lysozyme to be used as a sensitive biomarker to monitor exposure levels to the commonly used organophosphorus pesticide monocrotophos. Crystallization of lysozyme protein adduct with monocrotophos was also undertaken to understand the adduct formation mechanism at a molecular level. The binding of organophosphorus pesticides to lysozyme is one of the key steps in their mutagenicity. The formation and structural characterization of lysozyme adduct with monocrotophos was done using MALDI-TOFMS, fluorescence, UV/Vis spectroscopy, circular dichroism, and X-ray diffraction studies. We report the crystal structure of lysozyme adduct with monocrotophos at 1.9 Å. It crystallized in the P43 space group with two monomers in one asymmetric unit having one molecule of monocrotophos bound to each protein chain. The results proved that the fluorescence quenching of lysozyme by monocrotophos is due to binding of monocrotophos with a tryptophan residue of lysozyme. Monocrotophos interacts most strongly with the Trp-108 and Asp-52 of lysozyme. The interactions of the monocrotophos molecule with the lysozyme suggest the formation of a stable adduct. In addition, the alteration of lysozyme secondary structure in the presence of monocrotophos was confirmed by circular dichroism and fluorescence inhibition of lysozyme by increasing monocrotophos and UV/Vis spectrophotometry. The formation of lysozyme adduct with monocrotophos was confirmed by MALDI-TOFMS.

Organizational Affiliation

Department of Chemistry, Alliance College of Engineering and Design, Alliance University, Bangalore, 562106, India, sramaraneni@yahoo.com.

Macromolecule Content

Total Structure Weight: 29.2 kDa
Atom Count: 2,268
Modeled Residue Count: 258
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, B	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MVH Query on MVH Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	methyl [4-(methylamino)-4-oxidanylidene-but-2-en-2-yl] hydrogen phosphate C₆ H₁₂ N O₅ P SBZAFHSOQLENTI-SNAWJCMRSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	E [auth B], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.229 (Depositor), 0.240 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.72	α = 90
b = 78.72	β = 90
c = 37.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Amaraneni, S.R.

Kumar, S.

Samudrala, G.

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2014-10-01
Changes: Database references
Version 1.2: 2017-08-09
Changes: Derived calculations, Other, Source and taxonomy
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary