7MBH | pdb_00007mbh

Structure of Human Enolase 2 in complex with phosphoserine

PDB DOI: https://doi.org/10.2210/pdb7MBH/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-31 Released: 2022-11-09
Deposition Author(s): Leonard, P.G., Hicks, K.G., Rutter, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

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

PubMed: 36893255 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abm3452
Primary Citation 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.

Calico Life Sciences LLC, South San Francisco, CA, USA.

Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Institute for Applied Cancer Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.

School of Computing, University of Utah, Salt Lake City, UT, USA.

Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA.

Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.

Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea.

Department of Chemistry, Boston University, Boston, MA, USA.

The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China.

Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK.

Department of Biology, Boston University, Boston, MA, USA.

Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.

Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany.

Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.

Dana-Farber Cancer Institute, Boston, MA, USA.

Department of Biochemistry, West Virginia University, Morgantown, WV, USA.

Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.

Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Pittsburgh, PA, USA.

Pittsburgh Liver Research Center, Pittsburgh, PA, USA.

Center for Metabolism and Mitochondrial Medicine, Pittsburgh, PA, USA.

Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Macromolecule Content

Total Structure Weight: 97.02 kDa
Atom Count: 7,008
Modeled Residue Count: 870
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-enolase	A, B	440	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09104
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SEP (Subject of Investigation/LOI) Query on SEP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	PHOSPHOSERINE C₃ H₈ N O₆ P BZQFBWGGLXLEPQ-REOHCLBHSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]