4OLP | pdb_00004olp

Ligand-free structure of the GrpU microcompartment shell protein from Pectobacterium wasabiae

• PDB DOI: https://doi.org/10.2210/pdb4OLP/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pectobacterium parmentieri WPP163
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-24 Released: 2014-07-30 
• Deposition Author(s): Wheatley, N.M., Thompson, M.C., Gidaniyan, S.D., Sawaya, M.R., Jorda, J., Yeates, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.267 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

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

Thompson, M.C., Wheatley, N.M., Jorda, J., Sawaya, M.R., Gidaniyan, S.D., Ahmed, H., Yang, Z., McCarty, K.N., Whitelegge, J.P., Yeates, T.O.

(2014) J Mol Biology 426: 3287-3304

• PubMed: 25102080 
• DOI: https://doi.org/10.1016/j.jmb.2014.07.018
• Primary Citation Related Structures: 
  4OLO, 4OLP


• PubMed 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
Molecular Biology Interdepartmental Ph.D. Program, 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.
Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA.
Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA.
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.49 kDa 
• Atom Count: 2,641 
• Modeled Residue Count: 337 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GrpU microcompartment shell protein	A, B, C, D	107	Pectobacterium parmentieri WPP163	Mutation(s): 0  Gene Names: Pecwa_4094

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.267 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.845	α = 90
b = 117.845	β = 90
c = 76.023	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Wheatley, N.M., Thompson, M.C., Gidaniyan, S.D., Sawaya, M.R., Jorda, J., Yeates, T.O.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2014-08-20
  Changes: Database references
• Version 1.2: 2014-09-17
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Refinement description