Crystal structure of LeuD from Methanococcus jannaschii

Eun Hye Lee; Yong Wook Cho; Kwang Yeon Hwang

doi:10.1016/j.bbrc.2012.01.125

Crystal structure of LeuD from Methanococcus jannaschii

Eun Hye Lee, Yong Wook Cho, Kwang Yeon Hwang

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

6 Citations (Scopus)

Abstract

3-Isopropylmalate/citramalate (IPM) isomerase catalyzes the second step in the leucine biosynthesis pathway. IPM isomerase from . Methanococcus jannaschii is a complex protein consisting of a large (MjLeuC) and a small subunit (MjLeuD). It has broad substrate specificity, unlike other bacterial IPM isomerases. In order to understand the reasons for this broad substrate specificity, we determined the crystal structure of . MjLeuD at a resolution of 2.0. å. The asymmetric unit contained 6 molecules of LeuD, including three homodimers. The overall structure had a β/β/α sandwich-fold consisting of 8 α-helices and 7 β-strands. The C-terminal helix, which is important in homodimer formation, showed conformational differences between two homodimer forms of . MjLeuD. In addition, we identified a hydrophobic residue (Val28) near the substrate recognition region that may explain the broad substrate specificity of IPM isomerase. Therefore, we suggest that LeuD proteins can be divided into 2 subfamilies, LeuD subfamilies 1 and 2, which show differences in overall structure and in the substrate recognition region.

Original language	English
Pages (from-to)	160-164
Number of pages	5
Journal	Biochemical and biophysical research communications
Volume	419
Issue number	2
DOIs	https://doi.org/10.1016/j.bbrc.2012.01.125
Publication status	Published - 2012 Mar 9

Bibliographical note

Funding Information:
We would like to thank KJ Kim and his staff for their assistance with collecting the X-ray diffraction data using the RIKEN Structural Genomics Beamline BL26B1 at SPring-8 and Photon Factory BL-1A. This work was supported by a Global Frontier Project Grant (NRF-M1AXA002-20110028397) from the National Research Foundation funded by the Ministry of Education, Science and Technology of Korea and partly supported by the Functional Proteomics Center, 21C Frontier Program, of the Korea Ministry of Science and Technology KYH was also supported by KIST grants.

Keywords

3-Isopropylmalate dehydratase
3-Isopropylmalate isomerase
Broad specificity
Crystal structure
LeuD
Small subunit

ASJC Scopus subject areas

Biophysics
Biochemistry
Molecular Biology
Cell Biology

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10.1016/j.bbrc.2012.01.125

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title = "Crystal structure of LeuD from Methanococcus jannaschii",

abstract = "3-Isopropylmalate/citramalate (IPM) isomerase catalyzes the second step in the leucine biosynthesis pathway. IPM isomerase from . Methanococcus jannaschii is a complex protein consisting of a large (MjLeuC) and a small subunit (MjLeuD). It has broad substrate specificity, unlike other bacterial IPM isomerases. In order to understand the reasons for this broad substrate specificity, we determined the crystal structure of . MjLeuD at a resolution of 2.0. {\aa}. The asymmetric unit contained 6 molecules of LeuD, including three homodimers. The overall structure had a β/β/α sandwich-fold consisting of 8 α-helices and 7 β-strands. The C-terminal helix, which is important in homodimer formation, showed conformational differences between two homodimer forms of . MjLeuD. In addition, we identified a hydrophobic residue (Val28) near the substrate recognition region that may explain the broad substrate specificity of IPM isomerase. Therefore, we suggest that LeuD proteins can be divided into 2 subfamilies, LeuD subfamilies 1 and 2, which show differences in overall structure and in the substrate recognition region.",

keywords = "3-Isopropylmalate dehydratase, 3-Isopropylmalate isomerase, Broad specificity, Crystal structure, LeuD, Small subunit",

author = "Lee, {Eun Hye} and Cho, {Yong Wook} and Hwang, {Kwang Yeon}",

note = "Funding Information: We would like to thank KJ Kim and his staff for their assistance with collecting the X-ray diffraction data using the RIKEN Structural Genomics Beamline BL26B1 at SPring-8 and Photon Factory BL-1A. This work was supported by a Global Frontier Project Grant (NRF-M1AXA002-20110028397) from the National Research Foundation funded by the Ministry of Education, Science and Technology of Korea and partly supported by the Functional Proteomics Center, 21C Frontier Program, of the Korea Ministry of Science and Technology KYH was also supported by KIST grants.",

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AU - Lee, Eun Hye

AU - Cho, Yong Wook

AU - Hwang, Kwang Yeon

N1 - Funding Information: We would like to thank KJ Kim and his staff for their assistance with collecting the X-ray diffraction data using the RIKEN Structural Genomics Beamline BL26B1 at SPring-8 and Photon Factory BL-1A. This work was supported by a Global Frontier Project Grant (NRF-M1AXA002-20110028397) from the National Research Foundation funded by the Ministry of Education, Science and Technology of Korea and partly supported by the Functional Proteomics Center, 21C Frontier Program, of the Korea Ministry of Science and Technology KYH was also supported by KIST grants.

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N2 - 3-Isopropylmalate/citramalate (IPM) isomerase catalyzes the second step in the leucine biosynthesis pathway. IPM isomerase from . Methanococcus jannaschii is a complex protein consisting of a large (MjLeuC) and a small subunit (MjLeuD). It has broad substrate specificity, unlike other bacterial IPM isomerases. In order to understand the reasons for this broad substrate specificity, we determined the crystal structure of . MjLeuD at a resolution of 2.0. å. The asymmetric unit contained 6 molecules of LeuD, including three homodimers. The overall structure had a β/β/α sandwich-fold consisting of 8 α-helices and 7 β-strands. The C-terminal helix, which is important in homodimer formation, showed conformational differences between two homodimer forms of . MjLeuD. In addition, we identified a hydrophobic residue (Val28) near the substrate recognition region that may explain the broad substrate specificity of IPM isomerase. Therefore, we suggest that LeuD proteins can be divided into 2 subfamilies, LeuD subfamilies 1 and 2, which show differences in overall structure and in the substrate recognition region.

AB - 3-Isopropylmalate/citramalate (IPM) isomerase catalyzes the second step in the leucine biosynthesis pathway. IPM isomerase from . Methanococcus jannaschii is a complex protein consisting of a large (MjLeuC) and a small subunit (MjLeuD). It has broad substrate specificity, unlike other bacterial IPM isomerases. In order to understand the reasons for this broad substrate specificity, we determined the crystal structure of . MjLeuD at a resolution of 2.0. å. The asymmetric unit contained 6 molecules of LeuD, including three homodimers. The overall structure had a β/β/α sandwich-fold consisting of 8 α-helices and 7 β-strands. The C-terminal helix, which is important in homodimer formation, showed conformational differences between two homodimer forms of . MjLeuD. In addition, we identified a hydrophobic residue (Val28) near the substrate recognition region that may explain the broad substrate specificity of IPM isomerase. Therefore, we suggest that LeuD proteins can be divided into 2 subfamilies, LeuD subfamilies 1 and 2, which show differences in overall structure and in the substrate recognition region.

KW - 3-Isopropylmalate dehydratase

KW - 3-Isopropylmalate isomerase

KW - Broad specificity

KW - Crystal structure

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KW - Small subunit

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IS - 2

ER -

Crystal structure of LeuD from Methanococcus jannaschii

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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