3GKN

Insights into the Alkyl Peroxide Reduction Activity of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate/Ligand Complex Structures

Summary for 3GKN

• Entry DOI: 10.2210/pdb3gkn/pdb
• Related: 3GKK 3GKM
• Descriptor: Bacterioferritin comigratory protein, NAPHTHALENE-2,6-DISULFONIC ACID, GLYCEROL, ... (5 entities in total)
• Functional Keywords: xanthomonas campestris, bcp, prx, atypical 2-cys, oxidoreductase
• Biological source: Xanthomonas campestris pv. campestris
• Total number of polymer chains: 2
• Total formula weight: 36785.46

Authors

Liao, S.-J. (deposition date: 2009-03-11, release date: 2009-06-16, Last modification date: 2023-11-01)

Primary citation

Liao, S.-J.,Yang, C.-Y.,Chin, K.-H.,Wang, A.H.-J.,Chou, S.-H.
Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structures
J.Mol.Biol., 390:951-966, 2009

PubMed Abstract: Considerable insights into the oxidoreduction activity of the Xanthomonas campestris bacterioferritin comigratory protein (XcBCP) have been obtained from trapped intermediate/ligand complex structures determined by X-ray crystallography. Multiple sequence alignment and enzyme assay indicate that XcBCP belongs to a subfamily of atypical 2-Cys peroxiredoxins (Prxs), containing a strictly conserved peroxidatic cysteine (C(P)48) and an unconserved resolving cysteine (C(R)84). Crystals at different states, i.e. Free_SH state, Intra_SS state, and Inter_SS state, were obtained by screening the XcBCP proteins from a double C48S/C84S mutant, a wild type, and a C48A mutant, respectively. A formate or an alkyl analog with two water molecules that mimic an alkyl peroxide substrate was found close to the active site of the Free_SH or Inter_SS state, respectively. Their global structures were found to contain a novel substrate-binding pocket capable of accommodating an alkyl chain of no less than 16 carbons. In addition, in the Intra_SS or Inter_SS state, substantial local unfolding or complete unfolding of the C(R)-helix was detected, with the C(P)-helix remaining essentially unchanged. This is in contrast to the earlier observation that the C(P)-helix exhibits local unfolding during disulfide bond formation in typical 2-Cys Prxs. These rich experimental data have enabled us to propose a pathway by which XcBCP carries out its oxidoreduction activity through the alternate opening and closing of the substrate entry channel and the disulfide-bond pocket.

PubMed: 19477183
DOI: 10.1016/j.jmb.2009.05.030

Experimental method

X-RAY DIFFRACTION (1.47 Å)