3G7K

Crystal Structure of Methylitaconate-delta-isomerase

PDB DOI: 10.2210/pdb3G7K/pdb

Classification: ISOMERASE
Organism(s): Eubacterium barkeri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-10 Released: 2009-07-21
Deposition Author(s): Messerschmidt, A., Macieira, S., Velarde, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri

Velarde, M., Macieira, S., Hilberg, M., Broker, G., Tu, S.-M., Golding, B.T., Pierik, A.J., Buckel, W., Messerschmidt, A.

(2009) J Mol Biol 391: 609-620

PubMed: 19559030 Search on PubMed
DOI: 10.1016/j.jmb.2009.06.052
Primary Citation of Related Structures:
3G7K

PubMed Abstract:

3-Methylitaconate-Delta-isomerase (Mii) participates in the nicotinate fermentation pathway of the anaerobic soil bacterium Eubacterium barkeri (order Clostridiales) by catalyzing the reversible conversion of (R)-3-methylitaconate (2-methylene-3-methylsuccinate) to 2,3-dimethylmaleate. The enzyme is also able to catalyze the isomerization of itaconate (methylenesuccinate) to citraconate (methylmaleate) with ca 10-fold higher K(m) but > 1000-fold lower k(cat). The gene mii from E. barkeri was cloned and expressed in Escherichia coli. The protein produced with a C-terminal Strep-tag exhibited the same specific activity as the wild-type enzyme. The crystal structure of Mii from E. barkeri has been solved at a resolution of 2.70 A. The asymmetric unit of the P2(1)2(1)2(1) unit cell with parameters a = 53.1 A, b = 142.3 A, and c = 228.4 A contains four molecules of Mii. The enzyme belongs to a group of isomerases with a common structural feature, the so-called diaminopimelate epimerase fold. The monomer of 380 amino acid residues has two topologically similar domains exhibiting an alpha/beta-fold. The active site is situated in a cleft between these domains. The four Mii molecules are arranged as a tetramer with 222 symmetry for the N-terminal domains. The C-terminal domains have different relative positions with respect to the N-terminal domains resulting in a closed conformation for molecule A and two distinct open conformations for molecules B and D. The C-terminal domain of molecule C is disordered. The Mii active site contains the putative catalytic residues Lys62 and Cys96, for which mechanistic roles are proposed based on a docking experiment of the Mii substrate complex. The active sites of Mii and the closely related PrpF, most likely a methylaconitate Delta-isomerase, have been compared. The overall architecture including the active-site Lys62, Cys96, His300, and Ser17 (Mii numbering) is similar. This positioning of (R)-3-methylitaconate allows Cys96 (as thiolate) to deprotonate C-3 and (as thiol) to donate a proton to the methylene carbon atom of the resulting allylic carbanion. Interestingly, the active site of isopentenyl diphosphate isomerase type I also contains a cysteine that cooperates with glutamate rather than lysine. It has been proposed that the initial step in this enzyme is a protonation generating a tertiary carbocation intermediate.

Organizational Affiliation:

Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methylitaconate isomerase	A, B, C, D	391	Eubacterium barkeri	Mutation(s): 0 Gene Names: mii EC: 5.3.3 (PDB Primary Data), 5.3.3.6 (UniProt)
UniProt
Find proteins for Q0QLE6 (Eubacterium barkeri) Explore Q0QLE6 Go to UniProtKB: Q0QLE6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0QLE6
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Reference Sequence