4P2S

Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to Assembly of the Shell of the Pdu Microcompartment

PDB DOI: https://doi.org/10.2210/pdb4P2S/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Saintpaul str. SARA26
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-03-03 Released: 2014-05-14
Deposition Author(s): Sinha, S., Cheng, S., Sung, Y.W., McNamara, D.E., Sawaya, M.R., Yeates, T.O., Bobik, T.A.
Funding Organization(s): National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.209
R-Value Work: 0.194
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

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

Literature

Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to Assembly of the Shell of the Pdu Microcompartment.

Sinha, S., Cheng, S., Sung, Y.W., McNamara, D.E., Sawaya, M.R., Yeates, T.O., Bobik, T.A.

(2014) J Mol Biol 426: 2328

PubMed: 24747050 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2014.04.012
Primary Citation of Related Structures:
4P2S, 4PPD

PubMed Abstract:
Bacterial microcompartments (MCPs) are the simplest organelles known. They function to enhance metabolic pathways by confining several related enzymes inside an all-protein envelope called the shell. In this study, we investigated the factors that govern MCP assembly by performing scanning mutagenesis on the surface residues of PduA, a major shell protein of the MCP used for 1,2-propanediol degradation. Biochemical, genetic, and structural analysis of 20 mutants allowed us to determine that PduA K26, N29, and R79 are crucial residues that stabilize the shell of the 1,2-propanediol MCP. In addition, we identify two PduA mutants (K37A and K55A) that impair MCP function most likely by altering the permeability of its protein shell. These are the first studies to examine the phenotypic effects of shell protein structural mutations in an MCP system. The findings reported here may be applicable to engineering protein containers with improved stability for biotechnology applications.

Organizational Affiliation

Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.

Macromolecule Content

Total Structure Weight: 95.8 kDa
Atom Count: 5,989
Modelled Residue Count: 792
Deposited Residue Count: 909
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative propanediol utilization protein PduA	A, B, C, D, E A, B, C, D, E, F, G, H, I	101	Salmonella enterica subsp. enterica serovar Saintpaul str. SARA26	Mutation(s): 1 Gene Names: SES26_19178
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D]	R [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain V [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain V [auth H]	J [auth A], K [auth A], O [auth D], P [auth D], V [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth D] Focus chain P [auth D] Focus chain V [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth D] Focus chain P [auth D] Focus chain V [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G]	L [auth A] M [auth A] N [auth B] Q [auth D] S [auth G] L [auth A], M [auth A], N [auth B], Q [auth D], S [auth G], T [auth G], U [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain Q [auth D] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain Q [auth D] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G]