PDBsum entry 4ltm

Oxidoreductase

PDB id: 4ltm

Contents

Protein chain

187 a.a.

Ligands

FMN ×2

SO4

Waters ×91

PDB id:

4ltm

Name:

Oxidoreductase

Title:

Crystal structures of nadh:fmn oxidoreductase (emob) - fmn complex

Structure:

Nadh-dependent fmn reductase. Chain: a. Synonym: emob. Engineered: yes

Source:

Edta-degrading bacterium bnc1. Organism_taxid: 85561. Gene: emob. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å R-factor: 0.198 R-free: 0.204

Authors:

M.S.Nissen,B.Youn,B.D.Knowles,J.W.Ballinger,S.Jun,S.M.Belchik,L.Xun, C.Kang

Key ref:

M.S.Nissen et al. (2008). Crystal Structures of NADH:FMN Oxidoreductase (EmoB) at Different Stages of Catalysis. J Biol Chem, 283, 28710-28720. PubMed id: 18701448 DOI: 10.1074/jbc.M804535200

Date:

23-Jul-13 Release date: 07-Aug-13

Supersedes:

2vzh

Protein chain

Q9F9T2  (Q9F9T2_9PROT) -  NADH-dependent FMN reductase from EDTA-degrading bacterium BNC1

Seq: 197 a.a.

Struc: 187 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.5.1.42 - Fmn reductase (NADH).
• Reaction: FMNH2 + NAD⁺ = FMN + NADH + 2 H⁺

FMNH2 (Bound ligand (Het Group name = FMN) corresponds exactly) + NAD(+) = FMN + NADH + 2 × H(+)

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

reference

DOI no: 10.1074/jbc.M804535200

J Biol Chem 283:28710-28720 (2008)

PubMed id: 18701448

Crystal Structures of NADH:FMN Oxidoreductase (EmoB) at Different Stages of Catalysis.

M.S.Nissen, B.Youn, B.D.Knowles, J.W.Ballinger, S.Y.Jun, S.M.Belchik, L.Xun, C.Kang.

ABSTRACT

EDTA has become a major organic pollutant in the environment because of its extreme usage and resistance to biodegradation. Recently, two critical enzymes, EDTA monooxygenase (EmoA) and NADH:FMN oxidoreductase (EmoB), belonging to the newly established two-component flavin-diffusible monooxygenase family, were identified in the EDTA degradation pathway in Mesorhizobium sp. BNC1. EmoA is an FMNH(2)-dependent enzyme that requires EmoB to provide FMNH(2) for the conversion of EDTA to ethylenediaminediacetate. To understand the molecular basis of this FMN-mediated reaction, the crystal structures of the apo-form, FMN.FMN complex, and FMN.NADH complex of EmoB were determined at 2.5A resolution. The structure of EmoB is a homotetramer consisting of four alpha/beta-single-domain monomers of five parallel beta-strands flanked by five alpha-helices, which is quite different from those of other known two-component flavin-diffusible monooxygenase family members, such as PheA2 and HpaC, in terms of both tertiary and quaternary structures. For the first time, the crystal structures of both the FMN.FMN and FMN.NADH complexes of an NADH:FMN oxidoreductase were determined. Two stacked isoalloxazine rings and nicotinamide/isoalloxazine rings were at a proper distance for hydride transfer. The structures indicated a ping-pong reaction mechanism, which was confirmed by activity assays. Thus, the structural data offer detailed mechanistic information for hydride transfer between NADH to an enzyme-bound FMN and between the bound FMNH(2) and a diffusible FMN.

Selected figure(s)

Figure 1.
EDTA and nitrilotriacetate (a structural homolog of EDTA) degradation pathway. The enzymes are EDTA monooxygenase (encoded by emoA), NADH:FMN oxidoreductase (emoB), and ethylenediaminediacetate/iminodiacetate oxygenase (idaA). Each enzymatic step removes an acetate group as a glyoxylate. ED3A, ethylenediaminetriacetate; EDDA, ethylenediaminediacetate; EDMA, ethylenediaminemonoacetate; ED, ethylenediamine; NTA, nitrilotriacetate; IDA, iminodiacetate; Gly, glycine.

Figure 5.
Measurement of FMN, riboflavin, or NADH binding by ITC experiments. The trend of heat released by serial injections of FMN (▪), riboflavin (▾), or NADH (•) into EmoB was monitored. FMN showed the typical heat-releasing pattern. Neither riboflavin nor NADH had any detectable heat-releasing events upon injections. Solid lines represent the least-square fits of the data using a single-site binding model.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 28710-28720) copyright 2008.

Figures were selected by an automated process.