9C8B

Minimal PutA proline dehydrogenase domain (design #2) with the FAD N5 modified with propanal resulting from inactivation with N-allylglycine (replicate #2)

PDB DOI: https://doi.org/10.2210/pdb9C8B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti SM11
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-12 Released: 2024-10-30
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: 0.191
R-Value Work: 0.168
R-Value Observed: 0.169

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

Noncovalent Inhibition and Covalent Inactivation of Proline Dehydrogenase by Analogs of N -Propargylglycine.

Tanner, J.J., Ji, J., Bogner, A.N., Scott, G.K., Patel, S.M., Seravalli, J., Gates, K.S., Benz, C.C., Becker, D.F.

(2024) Biochemistry 63: 2855-2867

PubMed: 39437336 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.4c00429
Primary Citation of Related Structures:
8UPZ, 8UQ0, 8UQ1, 9C8A, 9C8B, 9C8C

PubMed Abstract:
The flavoenzyme proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the oxidation of l-proline to Δ ¹-pyrroline-5-carboxylate. The enzyme is a target for chemical probe discovery because of its role in the metabolism of certain cancer cells. N -propargylglycine is the first and best characterized mechanism-based covalent inactivator of PRODH. This compound consists of a recognition module (glycine) that directs the inactivator to the active site and an alkyne warhead that reacts with the FAD after oxidative activation, leading to covalent modification of the FAD N5 atom. Here we report structural and kinetic data on analogs of N -propargylglycine with the goals of understanding the initial docking step of the inactivation mechanism and to test the allyl group as a warhead. The crystal structures of PRODH complexed with unreactive analogs in which N is replaced by S show how the recognition module mimics the substrate proline by forming ion pairs with conserved arginine and lysine residues. Further, the C atom adjacent to the alkyne warhead is optimally positioned for hydride transfer to the FAD, providing the structural basis for the first bond-breaking step of the inactivation mechanism. The structures also suggest new strategies for designing improved N -propargylglycine analogs. N -allylglycine, which consists of a glycine recognition module and allyl warhead, is shown to be a covalent inactivator; however, it is less efficient than N -propargylglycine in both enzyme inactivation and cellular assays. Crystal structures of the N -allylglycine-inactivated enzyme are consistent with covalent modification of the N5 by propanal.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 91.02 kDa
Atom Count: 6,520
Modelled Residue Count: 764
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein PutA	A, B	396	Sinorhizobium meliloti SM11	Mutation(s): 0 Gene Names: putA, SM11_chr0102 EC: 1.5.5.2 (PDB Primary Data), 1.2.1.88 (PDB Primary Data)
UniProt
Find proteins for F7X6I3 (Sinorhizobium meliloti (strain SM11)) Explore F7X6I3 Go to UniProtKB: F7X6I3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F7X6I3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA (Subject of Investigation/LOI) Query on FDA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
CBG (Subject of Investigation/LOI) Query on CBG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	PROPANAL C₃ H₆ O NBBJYMSMWIIQGU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]