2IAQ | pdb_00002iaq

Crystal structure of squid ganglion DFPase S271A mutant

PDB DOI: https://doi.org/10.2210/pdb2IAQ/pdb

Classification: HYDROLASE
Organism(s): Loligo vulgaris
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-09-08 Released: 2006-09-26
Deposition Author(s): Scharff, E.I., Koepke, J., Fritzsch, G., Luecke, C., Rueterjans, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.233 (Depositor)
R-Value Work:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris

Scharff, E.I., Koepke, J., Fritzsch, G., Luecke, C., Rueterjans, H.

(2001) Structure 9: 493-502

PubMed: 11435114 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(01)00610-4
Primary Citation Related Structures:
1E1A, 2IAO, 2IAP, 2IAQ, 2IAR, 2IAS, 2IAT, 2IAU

PubMed Abstract:
Phosphotriesterases (PTE) are enzymes capable of detoxifying organophosphate-based chemical warfare agents by hydrolysis. One subclass of these enzymes comprises the family of diisopropylfluorophosphatases (DFPases). The DFPase reported here was originally isolated from squid head ganglion of Loligo vulgaris and can be characterized as squid-type DFPase. It is capable of hydrolyzing the organophosphates diisopropylfluorophosphate, soman, sarin, tabun, and cyclosarin. Crystals were grown of both the native and the selenomethionine-labeled enzyme. The X-ray crystal structure of the DFPase from Loligo vulgaris has been solved by MAD phasing and refined to a crystallographic R value of 17.6% at a final resolution of 1.8 A. Using site-directed mutagenesis, we have structurally and functionally characterized essential residues in the active site of the enzyme. The crystal structure of the DFPase from Loligo vulgaris is the first example of a structural characterization of a squid-type DFPase and the second crystal structure of a PTE determined to date. Therefore, it may serve as a structural model for squid-type DFPases in general. The overall structure of this protein represents a six-fold beta propeller with two calcium ions bound in a central water-filled tunnel. The consensus motif found in the blades of this beta propeller has not yet been observed in other beta propeller structures. Based on the results obtained from mutants of active-site residues, a mechanistic model for the DFP hydrolysis has been developed.

Organizational Affiliation

Institute of Biophysical Chemistry, Johann Wolfgang Goethe-University, Marie-Curie-Strasse 9, D-60439, Frankfurt/Main, Germany.

Macromolecule Content

Total Structure Weight: 34.92 kDa
Atom Count: 2,864
Modeled Residue Count: 312
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diisopropylfluorophosphatase	A	312	Loligo vulgaris	Mutation(s): 1 EC: 3.1.8.2 (PDB Primary Data), 3.8.2.2 (UniProt)
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris) Explore Q7SIG4 Go to UniProtKB: Q7SIG4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]