title: Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.
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.
authors: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, People's Republic of China.
authors: Xiaolu
authors: X
authors: Li
authors: Wei
authors: W
authors: Zhuo
authors: Jie
authors: J
authors: Yu
authors: Jingpeng
authors: J
authors: Ge
authors: Jinke
authors: J
authors: Gu
authors: Yue
authors: Y
authors: Feng
authors: Maojun
authors: M
authors: Yang
authors: Linfang
authors: L
authors: Wang
authors: Na
authors: N
authors: Wang
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000737:chemistry* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D009532:Nickel / Q000737:chemistry / Q000378:metabolism / Q000502:physiology; D011485:Protein Binding; D017510:Protein Folding; D013379:Substrate Specificity / Q000502:physiology; D046968:Thermoanaerobacter / Q000737:chemistry / Q000378:metabolism / Q000502:physiology
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D004151:Dipeptides; D007506:Iron-Sulfur Proteins; D026901:Membrane Transport Proteins; D009532:Nickel
keywords: ABC transporters; dipeptide permease; iron–sulfur clusters; nucleotide-binding domains