4YKF

Crystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NADH from Escherichia coli

Summary for 4YKF

• Entry DOI: 10.2210/pdb4ykf/pdb
• Related: 4YKG
• Descriptor: Alkyl hydroperoxide reductase subunit F, FLAVIN-ADENINE DINUCLEOTIDE, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ... (8 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Escherichia coli K12
• Total number of polymer chains: 1
• Total formula weight: 59361.54

Authors

Kamariah, N.,Manimekalai, M.S.S.,Gruber, G.,Eisenhaber, F.,Eisenhaber, B. (deposition date: 2015-03-04, release date: 2015-07-15, Last modification date: 2024-10-23)

Primary citation

Kamariah, N.,Manimekalai, M.S.S.,Nartey, W.,Eisenhaber, F.,Eisenhaber, B.,Gruber, G.
Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps
Biochim.Biophys.Acta, 1847:1139-1152, 2015

PubMed Abstract: Redox homeostasis is significant for the survival of pro- and eukaryotic cells and is crucial for defense against reactive oxygen species like superoxide and hydrogen peroxide. In Escherichia coli, the reduction of peroxides occurs via the redox active disulfide center of the alkyl hydroperoxide reductase C subunit (AhpC), whose reduced state becomes restored by AhpF. The 57kDa EcAhpF contains an N-terminal domain (NTD), which catalyzes the electron transfer from NADH via an FAD of the C-terminal domain into EcAhpC. The NTD is connected to the C-terminal domain via a linker. Here, the first crystal structure of E. coli AhpF bound with NADH and NAD(+) has been determined at 2.5Å and 2.4Å resolution, respectively. The NADH-bound form of EcAhpF reveals that the NADH-binding domain is required to alter its conformation to bring a bound NADH to the re-face of the isoalloxazine ring of the flavin, and thereby render the NADH-domain dithiol center accessible to the NTD disulfide center for electron transfer. The NAD(+)-bound form of EcAhpF shows conformational differences for the nicotinamide end moieties and its interacting residue M467, which is proposed to represent an intermediate product-release conformation. In addition, the structural alterations in EcAhpF due to NADH- and NAD(+)-binding in solution are shown by small angle X-ray scattering studies. The EcAhpF is revealed to adopt many intermediate conformations in solution to facilitate the electron transfer from the substrate NADH to the C-terminal domain, and subsequently to the NTD of EcAhpF for the final step of AhpC reduction.

PubMed: 26092085
DOI: 10.1016/j.bbabio.2015.06.011

Experimental method

X-RAY DIFFRACTION (2.5 Å)