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PDBsum entry 3gfh

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protein metals Protein-protein interface(s) links
Structural protein PDB id
3gfh
Jmol
Contents
Protein chains
214 a.a. *
Metals
_HG ×2
Waters ×171
* Residue conservation analysis
PDB id:
3gfh
Name: Structural protein
Title: Crystal structure of eutl shell protein of the bacterial ethanolamine micrompartment
Structure: Ethanolamine utilization protein eutl. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: b2439, eut-l, eutl, jw2432, yffj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.223     R-free:   0.278
Authors: M.Sagermann,K.Nikolakakis,A.Ohtaki
Key ref:
M.Sagermann et al. (2009). Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Proc Natl Acad Sci U S A, 106, 8883-8887. PubMed id: 19451619 DOI: 10.1073/pnas.0902324106
Date:
26-Feb-09     Release date:   21-Jul-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P76541  (EUTL_ECOLI) -  Ethanolamine utilization protein EutL
Seq:
Struc:
219 a.a.
214 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ethanolamine degradation polyhedral organelle   1 term 
  Biological process     response to external stimulus   2 terms 
  Biochemical function     structural molecule activity     2 terms  

 

 
DOI no: 10.1073/pnas.0902324106 Proc Natl Acad Sci U S A 106:8883-8887 (2009)
PubMed id: 19451619  
 
 
Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment.
M.Sagermann, A.Ohtaki, K.Nikolakakis.
 
  ABSTRACT  
 
Bacterial microcompartments (BMCs) are specialized organelles that use proteinaceous membranes to confine chemical reaction spaces. The ethanolamine ammonialyase microcompartment of Escherichia coli represents such a class of cytosolic organelles that enables bacteria to survive on small organic molecules such as ethanolamine as the sole source for carbon and nitrogen. We present here the crystal structure of the shell protein EutL at 2.2-A resolution. With 219 residues, it is the largest representative of this BMC's shell proteins. In the crystal, EutL forms a trimer that exhibits a hexagonally shaped tile structure. The tiles arrange into a tightly packed 2D array that is likely to resemble the proteinaceous membrane of the intact BMC. In contrast to other BMC shell proteins, which have only 1 pore per tile, EutL exhibits 3 pores per tile, thereby significantly increasing the overall porosity of this protein membrane. Each of the individual pores is lined with negatively charged residues and aromatic residues that are proposed to facilitate passive transport of specific solutes. The characteristic shape of the hexagonal tile, which is also found in the microcompartments of carbon-fixating bacteria, may present an inherent and fundamental building unit that may provide a general explanation for the formation of differently sized microcompartments.
 
  Selected figure(s)  
 
Figure 2.
Ribbon diagram of the structures of PduU [PDB ID code 3CGI (only residues 16–122 are shown for clarity)], EutL (C-terminal domain between residues 110 and 216), and Ccmk1 (PDB ID code 3BN4). The structures are displayed in rainbow coloring starting from the N terminus in blue in each case. Helix 1 of EutL is less regularly folded and consists of only 1 helix turn. Even though the overall fold of all proteins is very similar, the order of secondary structure elements is different. Whereas the structures EutL and PduU begin with and N-terminal β-strand (arrows), in the structure of Ccmk1 this strand and former helix 1 are now positioned at the C terminus.
Figure 5.
Representation of the solvent-accessible surface areas of EutL (Left), EutN (Center), and Ccmk1 (Right). In each structure, the monomers are colored differently. Even though EutN is also a hexameric structure, it displays an asymmetric central pore in contrast to Ccmk1. Despite the different functions and origin, all of the structures exhibit a hexagonal tile structure of very similar dimensions and shape.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21315581 T.O.Yeates, M.C.Thompson, and T.A.Bobik (2011).
The protein shells of bacterial microcompartment organelles.
  Curr Opin Struct Biol, 21, 223-231.  
20825353 C.A.Kerfeld, S.Heinhorst, and G.C.Cannon (2010).
Bacterial microcompartments.
  Annu Rev Microbiol, 64, 391-408.  
20308536 C.Fan, S.Cheng, Y.Liu, C.M.Escobar, C.S.Crowley, R.E.Jefferson, T.O.Yeates, and T.A.Bobik (2010).
Short N-terminal sequences package proteins into bacterial microcompartments.
  Proc Natl Acad Sci U S A, 107, 7509-7514.  
20234377 D.A.Garsin (2010).
Ethanolamine utilization in bacterial pathogens: roles and regulation.
  Nat Rev Microbiol, 8, 290-295.  
21046341 F.P.Bologna, V.A.Campos-Bermudez, D.D.Saavedra, C.S.Andreo, and M.F.Drincovich (2010).
Characterization of Escherichia coli EutD: a phosphotransacetylase of the ethanolamine operon.
  J Microbiol, 48, 629-636.  
20044574 S.Tanaka, M.R.Sawaya, and T.O.Yeates (2010).
Structure and mechanisms of a protein-based organelle in Escherichia coli.
  Science, 327, 81-84.
PDB codes: 3i6p 3i71 3i82 3i87 3i96 3ia0
20192762 T.O.Yeates, C.S.Crowley, and S.Tanaka (2010).
Bacterial microcompartment organelles: protein shell structure and evolution.
  Annu Rev Biophys, 39, 185-205.  
19844578 F.Cai, B.B.Menon, G.C.Cannon, K.J.Curry, J.M.Shively, and S.Heinhorst (2009).
The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier.
  PLoS One, 4, e7521.  
19844993 K.A.Dryden, C.S.Crowley, S.Tanaka, T.O.Yeates, and M.Yeager (2009).
Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals.
  Protein Sci, 18, 2629-2635.  
19690376 Y.Tsai, M.R.Sawaya, and T.O.Yeates (2009).
Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C.
  Acta Crystallogr D Biol Crystallogr, 65, 980-988.
PDB code: 3h8y
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.