Crystal Structure of a New Type of NADPH-Dependent Quinone Oxidoreductase (QOR2) from Escherichia coli

In Kwon Kim; Hyung Soon Yim; Min Kyu Kim; Dong Won Kim; Young Min Kim; Sun Shin Cha; Sa Ouk Kang

doi:10.1016/j.jmb.2008.04.003

Crystal Structure of a New Type of NADPH-Dependent Quinone Oxidoreductase (QOR2) from Escherichia coli

In Kwon Kim, Hyung Soon Yim, Min Kyu Kim, Dong Won Kim, Young Min Kim, Sun Shin Cha, Sa Ouk Kang

Department of Chemistry & Nanoscience

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Abstract

Escherichia coli QOR2 [NAD(P)H-dependent quinone oxidoreductase; a ytfG gene product], which catalyzes two-electron reduction of methyl-1,4-benzoquinone, is a new type of quinone-reducing enzyme with distinct primary sequence and oligomeric conformation from previously known quinone oxidoreductases. The crystal structures of native QOR2 and the QOR2-NADPH (nicotinamide adenine dinucleotide phosphate, reduced form) complex reveal that QOR2 consists of two domains (N-domain and C-domain) resembling those of NmrA, a negative transcriptional regulator that belongs to the short-chain dehydrogenase/reductase family. The N-domain, which adopts the Rossmann fold, provides a platform for NADPH binding, whereas the C-domain, which contains a hydrophobic pocket connected to the NADPH-binding site, appears to play important roles in substrate binding. Asn143 near the NADPH-binding site has been identified to be involved in substrate binding and catalysis from structural and mutational analyses. Moreover, compared with wild-type strain, the qor2-overexpressing strain shows growth retardation and remarkable decrease in several enzymes involved in carbon metabolism, suggesting that QOR2 could play some physiological roles in addition to quinone reduction.

Original language	English
Pages (from-to)	372-384
Number of pages	13
Journal	Journal of Molecular Biology
Volume	379
Issue number	2
DOIs	https://doi.org/10.1016/j.jmb.2008.04.003
State	Published - 29 May 2008

Bibliographical note

Funding Information:
We thank Dr. Y.-J. Seok for valuable discussions on these experiments; Mr. H.I. Jung and Ms. S.M. Cho for assistance with the preparation of the manuscript; Drs. K.-S. Chae and S.-K. Chae for providing a cDNA library of As. Nidulans; and Dr. J.-H. Roe for providing a pTac3 expression vector. Work performed at the Seoul National University was supported by the 21C Frontier Microbial Genomics and Application Center Program, Ministry of Science and Technology (grant MG02-0201-001-1-0-0), Republic of Korea, and by research fellowship of the BK21 project. Work performed at the Korea Ocean Research and Development Institute was supported by a grant from the Functional Proteomics Center, the 21C Frontier Research and Development Program of the Korea Ministry of Science and Technology, Republic of Korea.

Keywords

NAD(P)H-dependent quinone oxidoreductase
QOR2
carbon metabolism
short-chain dehydrogenase/reductase family
transcriptional regulator

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10.1016/j.jmb.2008.04.003

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@article{2a90f204504a44879dc41693ea7e295b,

title = "Crystal Structure of a New Type of NADPH-Dependent Quinone Oxidoreductase (QOR2) from Escherichia coli",

abstract = "Escherichia coli QOR2 [NAD(P)H-dependent quinone oxidoreductase; a ytfG gene product], which catalyzes two-electron reduction of methyl-1,4-benzoquinone, is a new type of quinone-reducing enzyme with distinct primary sequence and oligomeric conformation from previously known quinone oxidoreductases. The crystal structures of native QOR2 and the QOR2-NADPH (nicotinamide adenine dinucleotide phosphate, reduced form) complex reveal that QOR2 consists of two domains (N-domain and C-domain) resembling those of NmrA, a negative transcriptional regulator that belongs to the short-chain dehydrogenase/reductase family. The N-domain, which adopts the Rossmann fold, provides a platform for NADPH binding, whereas the C-domain, which contains a hydrophobic pocket connected to the NADPH-binding site, appears to play important roles in substrate binding. Asn143 near the NADPH-binding site has been identified to be involved in substrate binding and catalysis from structural and mutational analyses. Moreover, compared with wild-type strain, the qor2-overexpressing strain shows growth retardation and remarkable decrease in several enzymes involved in carbon metabolism, suggesting that QOR2 could play some physiological roles in addition to quinone reduction.",

keywords = "NAD(P)H-dependent quinone oxidoreductase, QOR2, carbon metabolism, short-chain dehydrogenase/reductase family, transcriptional regulator",

author = "Kim, {In Kwon} and Yim, {Hyung Soon} and Kim, {Min Kyu} and Kim, {Dong Won} and Kim, {Young Min} and Cha, {Sun Shin} and Kang, {Sa Ouk}",

note = "Funding Information: We thank Dr. Y.-J. Seok for valuable discussions on these experiments; Mr. H.I. Jung and Ms. S.M. Cho for assistance with the preparation of the manuscript; Drs. K.-S. Chae and S.-K. Chae for providing a cDNA library of As. Nidulans; and Dr. J.-H. Roe for providing a pTac3 expression vector. Work performed at the Seoul National University was supported by the 21C Frontier Microbial Genomics and Application Center Program, Ministry of Science and Technology (grant MG02-0201-001-1-0-0), Republic of Korea, and by research fellowship of the BK21 project. Work performed at the Korea Ocean Research and Development Institute was supported by a grant from the Functional Proteomics Center, the 21C Frontier Research and Development Program of the Korea Ministry of Science and Technology, Republic of Korea.",

year = "2008",

month = may,

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doi = "10.1016/j.jmb.2008.04.003",

language = "English",

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T1 - Crystal Structure of a New Type of NADPH-Dependent Quinone Oxidoreductase (QOR2) from Escherichia coli

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AU - Yim, Hyung Soon

AU - Kim, Min Kyu

AU - Kim, Dong Won

AU - Kim, Young Min

AU - Cha, Sun Shin

AU - Kang, Sa Ouk

N1 - Funding Information: We thank Dr. Y.-J. Seok for valuable discussions on these experiments; Mr. H.I. Jung and Ms. S.M. Cho for assistance with the preparation of the manuscript; Drs. K.-S. Chae and S.-K. Chae for providing a cDNA library of As. Nidulans; and Dr. J.-H. Roe for providing a pTac3 expression vector. Work performed at the Seoul National University was supported by the 21C Frontier Microbial Genomics and Application Center Program, Ministry of Science and Technology (grant MG02-0201-001-1-0-0), Republic of Korea, and by research fellowship of the BK21 project. Work performed at the Korea Ocean Research and Development Institute was supported by a grant from the Functional Proteomics Center, the 21C Frontier Research and Development Program of the Korea Ministry of Science and Technology, Republic of Korea.

PY - 2008/5/29

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N2 - Escherichia coli QOR2 [NAD(P)H-dependent quinone oxidoreductase; a ytfG gene product], which catalyzes two-electron reduction of methyl-1,4-benzoquinone, is a new type of quinone-reducing enzyme with distinct primary sequence and oligomeric conformation from previously known quinone oxidoreductases. The crystal structures of native QOR2 and the QOR2-NADPH (nicotinamide adenine dinucleotide phosphate, reduced form) complex reveal that QOR2 consists of two domains (N-domain and C-domain) resembling those of NmrA, a negative transcriptional regulator that belongs to the short-chain dehydrogenase/reductase family. The N-domain, which adopts the Rossmann fold, provides a platform for NADPH binding, whereas the C-domain, which contains a hydrophobic pocket connected to the NADPH-binding site, appears to play important roles in substrate binding. Asn143 near the NADPH-binding site has been identified to be involved in substrate binding and catalysis from structural and mutational analyses. Moreover, compared with wild-type strain, the qor2-overexpressing strain shows growth retardation and remarkable decrease in several enzymes involved in carbon metabolism, suggesting that QOR2 could play some physiological roles in addition to quinone reduction.

AB - Escherichia coli QOR2 [NAD(P)H-dependent quinone oxidoreductase; a ytfG gene product], which catalyzes two-electron reduction of methyl-1,4-benzoquinone, is a new type of quinone-reducing enzyme with distinct primary sequence and oligomeric conformation from previously known quinone oxidoreductases. The crystal structures of native QOR2 and the QOR2-NADPH (nicotinamide adenine dinucleotide phosphate, reduced form) complex reveal that QOR2 consists of two domains (N-domain and C-domain) resembling those of NmrA, a negative transcriptional regulator that belongs to the short-chain dehydrogenase/reductase family. The N-domain, which adopts the Rossmann fold, provides a platform for NADPH binding, whereas the C-domain, which contains a hydrophobic pocket connected to the NADPH-binding site, appears to play important roles in substrate binding. Asn143 near the NADPH-binding site has been identified to be involved in substrate binding and catalysis from structural and mutational analyses. Moreover, compared with wild-type strain, the qor2-overexpressing strain shows growth retardation and remarkable decrease in several enzymes involved in carbon metabolism, suggesting that QOR2 could play some physiological roles in addition to quinone reduction.

KW - NAD(P)H-dependent quinone oxidoreductase

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KW - carbon metabolism

KW - short-chain dehydrogenase/reductase family

KW - transcriptional regulator

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SN - 0022-2836

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JF - Journal of Molecular Biology

IS - 2

ER -

Crystal Structure of a New Type of NADPH-Dependent Quinone Oxidoreductase (QOR2) from Escherichia coli

Abstract

Bibliographical note

Keywords

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