PDBsum entry 2pw0

Unknown function

PDB id: 2pw0

Contents

Protein chains

386 a.a. *

342 a.a. *

Ligands

EDO ×6

TRC ×2

Waters ×880

* Residue conservation analysis

PDB id:

2pw0

Name:

Unknown function

Title:

Crystal structure of trans-aconitate bound to methylaconitate isomerase prpf from shewanella oneidensis

Structure:

Prpf methylaconitate isomerase. Chain: a, b. Engineered: yes

Source:

Shewanella oneidensis. Organism_taxid: 70863. Gene: prpf. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.57Å R-factor: 0.204 R-free: 0.232

Authors:

G.S.Garvey,I.R.Rayment

Key ref:

G.S.Garvey et al. (2007). The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function. Protein Sci, 16, 1274-1284. PubMed id: 17567742 DOI: 10.1110/ps.072801907

Date:

10-May-07 Release date: 21-Aug-07

Protein chain

Q8EJW4  (PRPF_SHEON) -  2-methyl-aconitate isomerase from Shewanella oneidensis (strain MR-1)

Seq: 397 a.a.

Struc: 386 a.a.

Protein chain

Q8EJW4  (PRPF_SHEON) -  2-methyl-aconitate isomerase from Shewanella oneidensis (strain MR-1)

Seq: 397 a.a.

Struc: 342 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.5.3.3.- - ?????

DOI no: 10.1110/ps.072801907

Protein Sci 16:1274-1284 (2007)

PubMed id: 17567742

The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function.

G.S.Garvey, C.J.Rocco, J.C.Escalante-Semerena, I.Rayment.

ABSTRACT

In bacteria, the dehydration of 2-methylcitrate to yield 2-methylaconitate in the 2-methylcitric acid cycle is catalyzed by a cofactor-less (PrpD) enzyme or by an aconitase-like (AcnD) enzyme. Bacteria that use AcnD also require the function of the PrpF protein, whose function was previously unknown. To gain insights into the function of PrpF, the three-dimensional crystal structure of the PrpF protein from the bacterium Shewanella oneidensis was solved at 2.0 A resolution. The protein fold of PrpF is strikingly similar to those of the non-PLP-dependent diaminopimelate epimerase from Haemophilus influenzae, a putative proline racemase from Brucella melitensis, and to a recently deposited structure of a hypothetical protein from Pseudomonas aeruginosa. Results from in vitro studies show that PrpF isomerizes trans-aconitate to cis-aconitate. It is proposed that PrpF catalysis of the cis-trans isomerization proceeds through a base-catalyzed proton abstraction coupled with a rotation about C2-C3 bond of 2-methylaconitate, and that residue Lys73 is critical for PrpF function. The newly identified function of PrpF as a non-PLP-dependent isomerase, together with the fact that PrpD-containing bacteria do not require PrpF, suggest that the isomer of 2-methylaconitate that serves as a substrate of aconitase must have the same stereochemistry as that synthesized by PrpD. From this, it follows that the 2-methylaconitate isomer generated by AcnD is not a substrate of aconitase, and that PrpF is required to generate the correct isomer. As a consequence, the isomerase activity of PrpF may now be viewed as an integral part of the 2-methylcitric acid cycle.

Selected figure(s)

Figure 1.
Figure 1. Schematic representation of the 2-methylcitric acid cycle with

Figure 7.
Figure 7. Established mechanism for aconitate isomerase from P. putida

The above figures are reprinted by permission from the Protein Society: Protein Sci (2007, 16, 1274-1284) copyright 2007.

Figures were selected by an automated process.