9E5W | pdb_00009e5w

Proline utilization A (PutA) from Sinorhizobium meliloti inactivated by N-propargylglycine

PDB DOI: https://doi.org/10.2210/pdb9E5W/pdb

Classification: OXIDOREDUCTASE/INHIBITOR
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-28 Released: 2025-02-05
Deposition Author(s): Tanner, J.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.211 (Depositor), 0.208 (DCC)
R-Value Work:
0.191 (Depositor), 0.188 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Biochemical, structural, and cellular characterization of S-but-3-yn-2-ylglycine as a mechanism-based covalent inactivator of the flavoenzyme proline dehydrogenase.

Meeks, K.R., Ji, J., Scott, G.K., Campbell, A.C., Nix, J.C., Tadeo, A., Ellerby, L.M., Benz, C.C., Tanner, J.J.

(2025) Arch Biochem Biophys 765: 110319-110319

PubMed: 39870289 Search on PubMed
DOI: https://doi.org/10.1016/j.abb.2025.110319
Primary Citation Related Structures:
9D7L, 9E5W

PubMed Abstract:
The mitochondrial flavoenzymes proline dehydrogenase (PRODH) and hydroxyproline dehydrogenase (PRODH2) catalyze the first steps of proline and hydroxyproline catabolism, respectively. The enzymes are targets for chemical probe development because of their roles in cancer cell metabolism (PRODH) and primary hyperoxaluria (PRODH2). Mechanism-based inactivators of PRODH target the FAD by covalently modifying the N5 atom, with N-propargylglycine (NPPG) being the current best-in-class of this type of probe. Here we investigated a close analog of NPPG, but-3-yn-2-ylglycine (B32G), distinguished by having a methyl group adjacent to the ethynyl group of the propargyl warhead. UV-visible spectroscopy shows that a bacterial PRODH catalyzes the oxidation of the S-enantiomer of B32G, a necessary first step in mechanism-based inactivation. In contrast, the enzyme does not react with the R-enantiomer. Enzyme activity assays show that S-B32G inhibits bacterial PRODH in a time-dependent manner consistent with covalent inactivation; however, the inactivation efficiency is ∼600-times lower than NPPG. We generated the crystal structure of PRODH inactivated by S-B32G at 1.68 Å resolution and found that inactivation induces a covalent link between the FAD N5 and the ε-nitrogen of an active site lysine, confirming that S-B32G follows the same mechanism as NPPG. Despite its lower inactivation efficiency at the purified bacterial enzyme, S-B32G exhibited comparable activity to NPPG against PRODH and PRODH2 in human cells and mouse livers. Molecular modeling is used to rationalize the stereospecificity of B32G.

Organizational Affiliation

Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States.

Macromolecule Content

Total Structure Weight: 268.52 kDa
Atom Count: 19,524
Modeled Residue Count: 2,414
Deposited Residue Count: 2,470
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein PutA	A, B	1,235	Sinorhizobium meliloti	Mutation(s): 0 Gene Names: putA, SMc02181 EC: 1.5.5.2 (PDB Primary Data), 1.2.1.88 (PDB Primary Data)
UniProt
Find proteins for Q92SD7 (Rhizobium meliloti (strain 1021)) Explore Q92SD7 Go to UniProtKB: Q92SD7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92SD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P5F Query on P5F Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain C [auth A]	C [auth A], N [auth B]	N-propargylglycine-modified flavin adenine dinucleotide C₃₂ H₄₀ N₁₀ O₁₇ P₂ IRSTVKNHNHEQIM-RDJFLKOLSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B]	D [auth A], O [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B]	K [auth A], S [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain S [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	J [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]