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J Mol Biol. 2014 Sep 23;426(19):3287-3304. doi: 10.1016/j.jmb.2014.07.018. Epub 2014 Aug 4.

Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein.

Author information

1
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
2
Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, CA 90095, USA.
3
University of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
4
Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA.
5
Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA.
6
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA. Electronic address: yeates@mbi.ucla.edu.

Abstract

Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins [bacterial microcompartment (in reference to the shell protein domain)] assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date.

KEYWORDS:

BMC-domain; conformational polymorphism; glycyl-radical propanediol (Grp); metalloprotein; symmetry-breaking

PMID:
25102080
PMCID:
PMC4175982
DOI:
10.1016/j.jmb.2014.07.018
[Indexed for MEDLINE]
Free PMC Article
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