6UFP image
Deposition Date 2019-09-24
Release Date 2020-03-18
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6UFP
Keywords:
Title:
Structure of proline utilization A with the FAD covalently modified by L-thiazolidine-2-carboxylate and three cysteines (Cys46, Cys470, Cys638) modified to S,S-(2-HYDROXYETHYL)THIOCYSTEINE
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.74 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Bifunctional protein PutA
Gene (Uniprot):putA
Chain IDs:A
Chain Length:1235
Number of Molecules:1
Biological Source:Sinorhizobium meliloti (strain SM11)
Polymer Type:polypeptide(L)
Molecule:Bifunctional protein PutA
Gene (Uniprot):putA
Chain IDs:B
Chain Length:1235
Number of Molecules:1
Biological Source:Sinorhizobium meliloti (strain SM11)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CME A CYS modified residue
Primary Citation
Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate.
Acs Chem.Biol. 15 936 944 (2020)
PMID: 32159324 DOI: 10.1021/acschembio.9b00935

Abstact

Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the FAD-dependent 2-electron oxidation of l-proline to Δ1-pyrroline-5-carboxylate. PRODH has emerged as a possible cancer therapy target, and thus the inhibition of PRODH is of interest. Here we show that the proline analogue thiazolidine-2-carboxylate (T2C) is a mechanism-based inactivator of PRODH. Structures of the bifunctional proline catabolic enzyme proline utilization A (PutA) determined from crystals grown in the presence of T2C feature strong electron density for a 5-membered ring species resembling l-T2C covalently bound to the N5 of the FAD in the PRODH domain. The modified FAD exhibits a large butterfly bend angle, indicating that the FAD is locked into the 2-electron reduced state. Reduction of the FAD is consistent with the crystals lacking the distinctive yellow color of the oxidized enzyme and stopped-flow kinetic data showing that T2C is a substrate for the PRODH domain of PutA. A mechanism is proposed in which PRODH catalyzes the oxidation of T2C at the C atom adjacent to the S atom of the thiazolidine ring (C5). Then, the N5 atom of the reduced FAD attacks the C5 of the oxidized T2C species, resulting in the covalent adduct observed in the crystal structure. To our knowledge, this is the first report of T2C inactivating (or inhibiting) PRODH or any other flavoenzyme. These results may inform the design of new mechanism-based inactivators of PRODH for use as chemical probes to study the roles of proline metabolism in cancer.

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Primary Citation of related structures