Cracking the shell of metabolosome

Allan Pang1, Martin J. Warren 2 and Richard W. Pickersgill 1 1 School of Biological and Chemical Sciences, Queen Mary University of London 2 School of Biosciences, University of Kent

For extensive info

Pang, A., M. J. Warren, R.W. Pickersgill. (2011). "Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site." Acta Crystallographica Section D: Biological Crystallography 67(2): 91-96.

What are metabolosomes?

Metabolosomes are icosahedral microcompartments which are able to catalyse metabolic processes; for example, the utilisation of propanediol as carbon source.

The pdu shell proteins

The propanediol utilisation (pdu) metabolosome is

1,2-propanediol 1,2-propanediol Cob(III)alamin PduS Cob(I)alamin PduGH AdoB12 PduO Propionaldehyde NAD+ NADH Propionyl-CoA PduW Propionate ATP PduP PduCDE PduQ 1-propanol

composed of several types of shell components; namely, PduA, PduB, PduJ, PduK, PduN, PduT, and PduU.

PduA PDB Code: 3NGK

PduU PDB Code: 3CGI

PduA and PduU have single BMC domain and form hexameric structure. The shell proteins are important in encapsulating various enzymes (marked red) as well as act as physical barrier, sequestering toxic intermediates like propionaldehyde. PduA is the main shell component and able to form a molecular tile. PduU has a unique -barrel that appears to block the central pore.

NAD+ NADH

METHYLCITRATE PATHWAY Propionyl-CoA PduL Propionyl-PO42ADP

Focus on PduT
PduT is one of the shell components of pdu metabolosome. The shell protein was successfully produced, purified and crystallised. The structure of PduT was solved using SAD phasing, exploiting the anomalous diffraction of the osmate ions. The final structure is refined to 1.86 resolution. Crystals grow as small hexagonal plates of about 0.1mm across

Key Structural Features of PduT

Duplicated BMC domain Tiling Property
Interaction between hexagonal shell PduT has a duplicated canonical BMC domain, as opposed to two known structures of Pdu shell proteins, PduA and PduU, which both have single BMC domain. As a result, PduT forms a trimeric assembly. With a pseudohexameric appearance, it is comparable to hexameric PduA and PduU.
PduT PDB Code: 3PAC

proteins are stabilised by conserved antiparallel lysine residues (marked yellow). When PduT is placed in the centre surrounded by the major shell component PduA, some of the anti-parallel lysine interactions are too loose while on others are too tight.

4Fe-4S cluster
However, the crystal structure we obtained does PduT has a reddish-orange color after purification. not contain an iron-sulfur cluster. Instead, the trimer has a wide central pore that implicates a 4Fe-4S cluster binding site. The 4Fe-4S cluster can be modelled in to the structure by coordinating Fe atoms with three Electron Paramagnetic Resonance spectra revealed the shell protein have a 4Fe-4S cluster. cysteines from each PduT subunit of the trimer. This leaves a free iron, which role could be to supply electrons to an associated microcompartment enzyme, PduS.