7TX2 | pdb_00007tx2

Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(4-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)butyl)amino)butanoic acid

PDB DOI: https://doi.org/10.2210/pdb7TX2/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-07 Released: 2023-02-15
Deposition Author(s): Harijan, R.K., Mahmoodi, N., Minnow, Y.V.T., Bonanno, J.B., Almo, S.C., Schramm, V.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Cell-Effective Transition-State Analogue of Phenylethanolamine N -Methyltransferase.

Mahmoodi, N., Minnow, Y.V.T., Harijan, R.K., Bedard, G.T., Schramm, V.L.

(2023) Biochemistry 62: 2257-2268

PubMed: 37467463 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.3c00103
Primary Citation Related Structures:
7TWU, 7TX2

PubMed Abstract:
Phenylethanolamine N -methyltransferase (PNMT) catalyzes the S -adenosyl-l-methionine (SAM)-dependent methylation of norepinephrine to form epinephrine. Epinephrine is implicated in the regulation of blood pressure, respiration, Alzheimer's disease, and post-traumatic stress disorder (PTSD). Transition-state (TS) analogues bind their target enzymes orders of magnitude more tightly than their substrates. A synthetic strategy for first-generation TS analogues of human PNMT (hPNMT) permitted structural analysis of hPNMT and revealed potential for second-generation inhibitors [Mahmoodi, N.; J. Am. Chem. Soc. 2020, 142, 14222-14233]. A second-generation TS analogue inhibitor of PNMT was designed, synthesized, and characterized to yield a K _i value of 1.2 nM. PNMT isothermal titration calorimetry (ITC) measurements of inhibitor 4 indicated a negative cooperative binding mechanism driven by large favorable entropic contributions and smaller enthalpic contributions. Cell-based assays with HEK293T cells expressing PNMT revealed a cell permeable, intracellular PNMT inhibitor with an IC ₅₀ value of 81 nM. Structural analysis demonstrated inhibitor 4 filling catalytic site regions to recapitulate both norepinephrine and SAM interactions. Conformation of the second-generation inhibitor in the catalytic site of PNMT improves contacts relative to those from the first-generation inhibitors. Inhibitor 4 demonstrates up to 51,000-fold specificity for PNMT relative to DNA and protein methyltransferases. Inhibitor 4 also exhibits a 12,000-fold specificity for PNMT over the α ₂-adrenoceptor.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.

Macromolecule Content

Total Structure Weight: 66.09 kDa
Atom Count: 4,249
Modeled Residue Count: 530
Deposited Residue Count: 588
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethanolamine N-methyltransferase	A, B	294	Homo sapiens	Mutation(s): 0 Gene Names: PNMT, PENT EC: 2.1.1.28
UniProt & NIH Common Fund Data Resources
Find proteins for P11086 (Homo sapiens) Explore P11086 Go to UniProtKB: P11086
PHAROS: P11086 GTEx: ENSG00000141744
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11086
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KNX (Subject of Investigation/LOI) Query on KNX Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	5'-([(3S)-3-amino-3-carboxypropyl]{4-[(4R)-7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl]butyl}amino)-5'-deoxyadenosine C₂₇ H₃₆ Cl₂ N₈ O₅ VHXBLPZYVDYOPX-STPVDRQBSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B]