PDBsum entry 6q1c

Metal transport

PDB id: 6q1c

Contents

Protein chain

259 a.a.

Waters ×166

PDB id:

6q1c

Name:

Metal transport

Title:

Apo yfea extracted from the e. Coli periplasm

Structure:

Periplasmic chelated iron-binding protein yfea. Chain: a. Engineered: yes

Source:

Yersinia pestis. Organism_taxid: 632. Gene: yfea, ypo2439, y1897, yp_2227. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.76Å R-factor: 0.194 R-free: 0.239

Authors:

C.D.Radka,S.L.Labiuk,L.J.Delucas,S.G.Aller

Key ref:

C.D.Radka et al. (2019). Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms. Acta Crystallogr D Struct Biol, 75, 831-840. PubMed id: 31478906 DOI: 10.1107/S2059798319010866

Date:

03-Aug-19 Release date: 04-Sep-19

Protein chain

Q56952  (YFEA_YERPE) -  Iron-binding protein YfeA from Yersinia pestis

Seq: 311 a.a.

Struc: 259 a.a.

DOI no: 10.1107/S2059798319010866

Acta Crystallogr D Struct Biol 75:831-840 (2019)

PubMed id: 31478906

Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms.

C.D.Radka, S.L.Labiuk, L.J.DeLucas, S.G.Aller.

ABSTRACT

In the structural biology of bacterial substrate-binding proteins (SBPs), a growing number of comparisons between substrate-bound and substrate-free forms of metal atom-binding (cluster A-I) SBPs have revealed minimal structural differences between forms. These observations contrast with SBPs that bind substrates such as amino acids or nucleic acids and may undergo >60° rigid-body rotations. Substrate transfer in these SBPs is described by a Venus flytrap model, although this model may not apply to all SBPs. In this report, structures are presented of substrate-free (apo) and reconstituted substrate-bound (holo) YfeA, a polyspecific cluster A-I SBP from Yersinia pestis. It is demonstrated that an apo cluster A-I SBP can be purified by fractionation when co-expressed with its cognate transporter, adding an alternative strategy to the mutagenesis or biochemical treatment used to generate other apo cluster A-I SBPs. The apo YfeA structure contains 111 disordered protein atoms in a mobile helix located in the flexible carboxy-terminal lobe. Metal binding triggers a 15-fold reduction in the solvent-accessible surface area of the metal-binding site and reordering of the 111 protein atoms in the mobile helix. The flexible lobe undergoes a 13.6° rigid-body rotation that is driven by a spring-hammer metal-binding mechanism. This asymmetric rigid-body rotation may be unique to metal atom-binding SBPs (i.e. clusters A-I, A-II and D-IV).