PDBsum entry 3cgi

Unknown function

PDB id: 3cgi

Contents

Protein chains

112 a.a. *

119 a.a. *

Waters ×165

* Residue conservation analysis

PDB id:

3cgi

Name:

Unknown function

Title:

Crystal structure of the pduu shell protein from the pdu microcompartment

Structure:

Propanediol utilization protein pduu. Chain: a, b, c, d. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 90371. Strain: lt2. Gene: pduu. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.205 R-free: 0.242

Authors:

C.S.Crowley,M.R.Sawaya,T.O.Yeates

Key ref:

C.S.Crowley et al. (2008). Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure, 16, 1324-1332. PubMed id: 18786396 DOI: 10.1016/j.str.2008.05.013

Date:

05-Mar-08 Release date: 02-Sep-08

Protein chains

P0A1D1  (PDUU_SALTY) -  Bacterial microcompartment shell protein PduU from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 116 a.a.

Struc: 112 a.a.

Protein chains

P0A1D1  (PDUU_SALTY) -  Bacterial microcompartment shell protein PduU from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 116 a.a.

Struc: 119 a.a.

DOI no: 10.1016/j.str.2008.05.013

Structure 16:1324-1332 (2008)

PubMed id: 18786396

Structure of the PduU shell protein from the Pdu microcompartment of Salmonella.

C.S.Crowley, M.R.Sawaya, T.A.Bobik, T.O.Yeates.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 1324-1332) copyright 2008.

Figures were selected by the author.