Structure of the dihydrolipoamide succinyltransferase (E2)
component of the human alpha-ketoglutarate dehydrogenase
complex (hKGDHc) revealed by cryo-EM and cross-linking mass
spectrometry: Implications for the overall hKGDHc structure

J 2021

Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure

NAGY, B., Martin POLÁK, O. OZOHANICS, Z. ZAMBO, E. SZABO et. al.

Basic information

Original name

Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure

Authors

NAGY, B., Martin POLÁK (203 Czech Republic, belonging to the institution), O. OZOHANICS, Z. ZAMBO, E. SZABO, A. HUBERT, F. JORDAN, Jiří NOVÁČEK (203 Czech Republic, guarantor, belonging to the institution), V. ADAM-VIZI and A. AMBRUS

Edition

Biochimica et Biophysica Acta - General Subjects, Amsterdam, Elsevier B.V. 2021, 0304-4165

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.117

RIV identification code

RIV/00216224:14740/21:00124433

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1016/j.bbagen.2021.129889

UT WoS

000640021000013

Keywords in English

alpha-Ketoglutarate dehydrogenase complex; 2-Oxoglutarate dehydrogenase complex; Dihydrolipoamide succinyltransferase; Cryo-electron microscopy; Cross-linking mass spectrometry

Abstract

V originále

Background: The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers. Methods: We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling. Results: We report the 2.9 angstrom resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc. Conclusions: The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 x 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly. General significance: The revealed structural information will support the future pharmacologically targeting of the hKGDHc.

Links

LM2018127, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

NAGY, B., Martin POLÁK, O. OZOHANICS, Z. ZAMBO, E. SZABO, A. HUBERT, F. JORDAN, Jiří NOVÁČEK, V. ADAM-VIZI and A. AMBRUS. Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure. Biochimica et Biophysica Acta - General Subjects. Amsterdam: Elsevier B.V., 2021, vol. 1865, No 6, p. 129889-129903. ISSN 0304-4165. Available from: https://dx.doi.org/10.1016/j.bbagen.2021.129889.

@article{1842560,
   author = {Nagy, B. and Polák, Martin and Ozohanics, O. and Zambo, Z. and Szabo, E. and Hubert, A. and Jordan, F. and Nováček, Jiří and AdamandVizi, V. and Ambrus, A.},
   article_location = {Amsterdam},
   article_number = {6},
   doi = {http://dx.doi.org/10.1016/j.bbagen.2021.129889},
   keywords = {alpha-Ketoglutarate dehydrogenase complex; 2-Oxoglutarate dehydrogenase complex; Dihydrolipoamide succinyltransferase; Cryo-electron microscopy; Cross-linking mass spectrometry},
   language = {eng},
   issn = {0304-4165},
   journal = {Biochimica et Biophysica Acta - General Subjects},
   title = {Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure},
   url = {https://www.sciencedirect.com/science/article/pii/S0304416521000477?via%3Dihub},
   volume = {1865},
   year = {2021}
}

TY  - JOUR
ID  - 1842560
AU  - Nagy, B. - Polák, Martin - Ozohanics, O. - Zambo, Z. - Szabo, E. - Hubert, A. - Jordan, F. - Nováček, Jiří - Adam-Vizi, V. - Ambrus, A.
PY  - 2021
TI  - Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure
JF  - Biochimica et Biophysica Acta - General Subjects
VL  - 1865
IS  - 6
SP  - 129889
EP  - 129889
PB  - Elsevier B.V.
SN  - 03044165
KW  - alpha-Ketoglutarate dehydrogenase complex
KW  - 2-Oxoglutarate dehydrogenase complex
KW  - Dihydrolipoamide succinyltransferase
KW  - Cryo-electron microscopy
KW  - Cross-linking mass spectrometry
UR  - https://www.sciencedirect.com/science/article/pii/S0304416521000477?via%3Dihub
N2  - Background: The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers. Methods: We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling. Results: We report the 2.9 angstrom resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc. Conclusions: The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 x 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly. General significance: The revealed structural information will support the future pharmacologically targeting of the hKGDHc.
ER  -

NAGY, B., Martin POLÁK, O. OZOHANICS, Z. ZAMBO, E. SZABO, A. HUBERT, F. JORDAN, Jiří NOVÁČEK, V. ADAM-VIZI and A. AMBRUS. Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure. \textit{Biochimica et Biophysica Acta - General Subjects}. Amsterdam: Elsevier B.V., 2021, vol.~1865, No~6, p.~129889-129903. ISSN~0304-4165. Available from: https://dx.doi.org/10.1016/j.bbagen.2021.129889.

Detailed Information on Publication Record