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PDBsum entry 3cgi
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Unknown function
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PDB id
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3cgi
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References listed in PDB file
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Key reference
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Title
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Structure of the pduu shell protein from the pdu microcompartment of salmonella.
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Authors
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C.S.Crowley,
M.R.Sawaya,
T.A.Bobik,
T.O.Yeates.
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Ref.
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Structure, 2008,
16,
1324-1332.
[DOI no: ]
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PubMed id
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Abstract
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The Pdu microcompartment is a proteinaceous, subcellular structure that serves
as an organelle for the metabolism of 1,2-propanediol in Salmonella enterica. It
encapsulates several related enzymes within a shell composed of a few thousand
protein subunits. Recent structural studies on the carboxysome, a related
microcompartment involved in CO(2) fixation, have concluded that the major shell
proteins from that microcompartment form hexamers that pack into layers
comprising the facets of the shell. Here we report the crystal structure of
PduU, a protein from the Pdu microcompartment, representing the first structure
of a shell protein from a noncarboxysome microcompartment. Though PduU is a
hexamer like other characterized shell proteins, it has undergone a circular
permutation leading to dramatic differences in the hexamer pore. In view of the
hypothesis that microcompartment metabolites diffuse across the outer shell
through these pores, the unique structure of PduU suggests the possibility of a
special functional role.
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Figure 2.
Figure 2. Crystal Structure of the PduU Shell Protein
(A
and B) (A) The PduU hexamer viewed along the sixfold axis and
(B) perpendicular to the sixfold axis with distinct protein
chains colored separately. The outline drawn around the hexamer
(A) illustrates its presumed packing in the microcompartment
shell among the other (more abundant) homologous shell protein
hexamers (e.g., PduA, PduB, PduB′, and PduJ). A prominent
feature of the PduU hexamer is the six-stranded, parallel
β-barrel formed by one N-terminal β strand from each monomer.
Whether this feature at the top of the hexamer faces out toward
the cytosol or toward the interior of the microcompartment has
not been established.
(C) Ribbon diagram depicting the PduU
monomer, colored from blue (N terminal) to red (C terminal).
Over residue positions 19–109, the chain adopts a variation of
the typical bacterial microcompartment (BMC) fold (Kerfeld et
al., 2005). The 18 amino-terminal and eight carboxy-terminal
residues form novel secondary structural elements.
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Figure 5.
Figure 5. Structure of the β-barrel Cap in PduU
(A and
B) Cutaway views showing the side chain packing within the two
hexamer β-barrels. The side chains (sticks) of Met[10],
Gln[12], and Tyr[14] are buried within the β-barrel. Owing to
steric restrictions, all Gln[12] side chains were modeled in two
alternating conformations: “up” toward the N terminus and
“down” toward the C terminus. Interchain hydrogen bonding
between upward-oriented Gln[12] side chains is present in the
configuration shown in (A) (dashed line).
(C) Stereo view
of the PduU β-barrel viewed from its C-terminal end. Gln[12]
and other interior side chains are illustrated. The
configurations shown in both panels are from the hexamer labeled
“1” in the crystal asymmetric unit.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2008,
16,
1324-1332)
copyright 2008.
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