4WKG

The crystal structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic coop-erativity

Summary for 4WKG

• Entry DOI: 10.2210/pdb4wkg/pdb
• Descriptor: Bifunctional polymyxin resistance protein ArnA, 2,3-DIHYDROXY-1,4-DITHIOBUTANE, ACETATE ION, ... (4 entities in total)
• Functional Keywords: arna, multi-drug resistance, mdr, polymyxin, dehydrogenase, transformylase, cooperativity, allosteric regulation, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 6
• Total formula weight: 446741.23

Authors

Grimm, C. (deposition date: 2014-10-02, release date: 2014-12-17, Last modification date: 2024-01-10)

Primary citation

Fischer, U.,Hertlein, S.,Grimm, C.
The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity.
Acta Crystallogr.,Sect.D, 71:687-696, 2015

PubMed Abstract: The bacterial protein ArnA is an essential enzyme in the pathway leading to the modification of lipid A with the pentose sugar 4-amino-4-deoxy-L-arabinose. This modification confers resistance to polymyxins, which are antibiotics that are used as a last resort to treat infections with multiple drug-resistant Gram-negative bacteria. ArnA contains two domains with distinct catalytic functions: a dehydrogenase domain and a transformylase domain. The protein forms homohexamers organized as a dimer of trimers. Here, the crystal structure of apo ArnA is presented and compared with its ATP- and UDP-glucuronic acid-bound counterparts. The comparison reveals major structural rearrangements in the dehydrogenase domain that lead to the formation of a previously unobserved binding pocket at the centre of each ArnA trimer in its apo state. In the crystal structure, this pocket is occupied by a DTT molecule. It is shown that formation of the pocket is linked to a cascade of structural rearrangements that emerge from the NAD(+)-binding site. Based on these findings, a small effector molecule is postulated that binds to the central pocket and modulates the catalytic properties of ArnA. Furthermore, the discovered conformational changes provide a mechanistic explanation for the strong cooperative effect recently reported for the ArnA dehydrogenase function.

PubMed: 25760615
DOI: 10.1107/S1399004714026686

Experimental method

X-RAY DIFFRACTION (2.7 Å)