6Q1C

Apo YfeA extracted from the E. coli periplasm

Summary for 6Q1C

• Entry DOI: 10.2210/pdb6q1c/pdb
• Descriptor: Periplasmic chelated iron-binding protein YfeA (2 entities in total)
• Functional Keywords: yersinia pestis, substrate binding protein, sbp, yfea, metal transport
• Biological source: Yersinia pestis
• Total number of polymer chains: 1
• Total formula weight: 34425.09

Authors

Radka, C.D.,Labiuk, S.L.,DeLucas, L.J.,Aller, S.G. (deposition date: 2019-08-03, release date: 2019-09-04, Last modification date: 2023-10-11)

Primary citation

Radka, C.D.,Labiuk, S.L.,DeLucas, L.J.,Aller, S.G.
Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms.
Acta Crystallogr D Struct Biol, 75:831-840, 2019

PubMed 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).

PubMed: 31478906
DOI: 10.1107/S2059798319010866

Experimental method

X-RAY DIFFRACTION (1.76 Å)