7MBH

Structure of Human Enolase 2 in complex with phosphoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-enolase
A, B
440Homo sapiensMutation(s): 0 
Gene Names: ENO2
EC: 4.2.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09104 (Homo sapiens)
Explore P09104 
Go to UniProtKB:  P09104
PHAROS:  P09104
GTEx:  ENSG00000111674 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09104
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SEP (Subject of Investigation/LOI)
Query on SEP

Download Ideal Coordinates CCD File 
H [auth B]PHOSPHOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.05α = 90
b = 108.38β = 90
c = 117.929γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM131854

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description