Crystal structure of recombinant human fumarase in complex with D-2-amino-3-phosphono-propionic acid

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.

Hicks, K.G.Cluntun, A.A.Schubert, H.L.Hackett, S.R.Berg, J.A.Leonard, P.G.Ajalla Aleixo, M.A.Zhou, Y.Bott, A.J.Salvatore, S.R.Chang, F.Blevins, A.Barta, P.Tilley, S.Leifer, A.Guzman, A.Arok, A.Fogarty, S.Winter, J.M.Ahn, H.C.Allen, K.N.Block, S.Cardoso, I.A.Ding, J.Dreveny, I.Gasper, W.C.Ho, Q.Matsuura, A.Palladino, M.J.Prajapati, S.Sun, P.Tittmann, K.Tolan, D.R.Unterlass, J.VanDemark, A.P.Vander Heiden, M.G.Webb, B.A.Yun, C.H.Zhao, P.Wang, B.Schopfer, F.J.Hill, C.P.Nonato, M.C.Muller, F.L.Cox, J.E.Rutter, J.

(2023) Science 379: 996-1003

  • DOI: https://doi.org/10.1126/science.abm3452
  • Primary Citation of Related Structures:  
    7LUB, 7MBH

  • PubMed Abstract: 

    Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.

  • Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fumarate hydratase, mitochondrial
A, B
466Homo sapiensMutation(s): 0 
Gene Names: FH
UniProt & NIH Common Fund Data Resources
Find proteins for P07954 (Homo sapiens)
Explore P07954 
Go to UniProtKB:  P07954
PHAROS:  P07954
GTEx:  ENSG00000091483 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07954
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.903α = 90
b = 190.903β = 90
c = 116.243γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2012/25075-0

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description