6H05

Cryo-electron microscopic structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex [residues 218-453]


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.Polak, M.Ozohanics, O.Zambo, Z.Szabo, E.Hubert, A.Jordan, F.Novacek, J.Adam-Vizi, V.Ambrus, A.

(2021) Biochim Biophys Acta Gen Subj 1865: 129889-129889

  • DOI: https://doi.org/10.1016/j.bbagen.2021.129889
  • Primary Citation of Related Structures:  
    6H05

  • PubMed Abstract: 

    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. 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. We report the 2.9 Å 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. The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 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. The revealed structural information will support the future pharmacologically targeting of the hKGDHc.


  • Organizational Affiliation

    Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial426Homo sapiensMutation(s): 0 
Gene Names: DLSTDLTS
EC: 2.3.1.61
UniProt & NIH Common Fund Data Resources
Find proteins for P36957 (Homo sapiens)
Explore P36957 
Go to UniProtKB:  P36957
GTEx:  ENSG00000119689 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36957
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hungarian Academy of SciencesHungaryMTA grant 02001 (to Vera Adam-Vizi)
Hungarian Academy of SciencesHungaryOTKA grant 112230 (to Vera Adam-Vizi)
Hungarian Academy of SciencesHungaryNAP grant KTIA_13_NAP-A-III/6 (to Vera Adam-Vizi)
Hungarian Academy of SciencesHungaryNAP 2 grant 2017-1.2.1-NKP- 2017-00002 (to Vera Adam-Vizi)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH-GM-050380 (to Frank Jordan)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH R15-GM116077 (to Frank Jordan)

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations