4FWI

Crystal structure of the nucleotide-binding domain of a dipeptide ABC transporter

Summary for 4FWI

• Entry DOI: 10.2210/pdb4fwi/pdb
• Descriptor: ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component, IRON/SULFUR CLUSTER, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: nbds, abc transporter, nucleotide binding, iron-sulfur cluster, transport protein
• Biological source: Thermoanaerobacter tengcongensis
• Total number of polymer chains: 1
• Total formula weight: 38366.02

Authors

Li, X.,Ge, J.,Yang, M.,Wang, N. (deposition date: 2012-07-01, release date: 2013-01-30, Last modification date: 2024-03-20)

Primary citation

Li, X.,Zhuo, W.,Yu, J.,Ge, J.,Gu, J.,Feng, Y.,Yang, M.,Wang, L.,Wang, N.
Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain
Acta Crystallogr.,Sect.D, 69:256-265, 2013

PubMed Abstract: Dipeptide permease (Dpp), which belongs to an ABC transport system, imports peptides consisting of two or three L-amino acids from the matrix to the cytoplasm in microbes. Previous studies have indicated that haem competes with dipeptides to bind DppA in vitro and in vivo and that the Dpp system can also translocate haem. Here, the crystal structure of DppD, the nucleotide-binding domain (NBD) of the ABC-type dipeptide/oligopeptide/nickel-transport system from Thermoanaerobacter tengcongensis, bound with ATP, Mg(2+) and a [4Fe-4S] iron-sulfur cluster is reported. The N-terminal domain of DppD shares a similar structural fold with the NBDs of other ABC transporters. Interestingly, the C-terminal domain of DppD contains a [4Fe-4S] cluster. The UV-visible absorbance spectrum of DppD was consistent with the presence of a [4Fe-4S] cluster. A search with DALI revealed that the [4Fe-4S] cluster-binding domain is a novel structural fold. Structural analysis and comparisons with other ABC transporters revealed that this iron-sulfur cluster may act as a mediator in substrate (dipeptide or haem) binding by electron transfer and may regulate the transport process in Dpp ABC transport systems. The crystal structure provides a basis for understanding the properties of ABC transporters and will be helpful in investigating the functions of NBDs in the regulation of ABC transporter activity.

PubMed: 23385461
DOI: 10.1107/S0907444912045180

Experimental method

X-RAY DIFFRACTION (2.892 Å)