PDBsum entry 4fwi

Transport protein

PDB id: 4fwi

Contents

Protein chain

310 a.a.

Ligands

SF4

ATP

Metals

_MG

PDB id:

4fwi

Name:

Transport protein

Title:

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

Structure:

Abc-type dipeptide/oligopeptide/nickel transport system, atpase component. Chain: b. Engineered: yes

Source:

Thermoanaerobacter tengcongensis. Organism_taxid: 273068. Strain: mb4. Gene: dppd. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.89Å R-factor: 0.215 R-free: 0.268

Authors:

X.Li,J.Ge,M.Yang,N.Wang

Key ref:

X.Li et al. (2013). Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain. Acta Crystallogr D Biol Crystallogr, 69, 256-265. PubMed id: 23385461

Date:

01-Jul-12 Release date: 30-Jan-13

Protein chain

Q8RDH4  (Q8RDH4_CALS4) -  Dipeptide transport ATP-binding protein DppD from Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)

Seq: 326 a.a.

Struc: 310 a.a.

Enzyme reactions

• Enzyme class: E.C.7.4.2.9 - ABC-type dipeptide transporter.
• Reaction: a dipeptide(out) + ATP + H2O = a dipeptide(in) + ADP + phosphate + H⁺

dipeptide(out) + ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + H2O = dipeptide(in) + ADP + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Acta Crystallogr D Biol Crystallogr 69:256-265 (2013)

PubMed id: 23385461

Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.

X.Li, W.Zhuo, J.Yu, J.Ge, J.Gu, Y.Feng, M.Yang, L.Wang, N.Wang.

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.