5CZJ

Crystal structure of HypD, a 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Sinorhizobium meliloti

Summary for 5CZJ

• Entry DOI: 10.2210/pdb5czj/pdb
• Descriptor: Dihydrodipicolinate synthase (2 entities in total)
• Functional Keywords: n-acetylneuraminate lyase sub-family, (alpha/beta)8 barrel, tim barrel, 4-hydroxy-proline metabolism, hydrolase
• Biological source: Rhizobium meliloti (strain 1021) (Ensifer meliloti)
• Total number of polymer chains: 2
• Total formula weight: 68971.05

Authors

Stogios, P.J.,Xu, X.,Savchenko, A. (deposition date: 2015-07-31, release date: 2016-02-03, Last modification date: 2023-09-27)

Primary citation

Chen, S.,White, C.E.,diCenzo, G.C.,Zhang, Y.,Stogios, P.J.,Savchenko, A.,Finan, T.M.
l-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti.
J.Bacteriol., 198:1171-1181, 2016

PubMed Abstract: Sinorhizobium meliloti forms N2-fixing root nodules on alfalfa, and as a free-living bacterium, it can grow on a very broad range of substrates, including l-proline and several related compounds, such as proline betaine, trans-4-hydroxy-l-proline (trans-4-l-Hyp), and cis-4-hydroxy-d-proline (cis-4-d-Hyp). Fourteen hyp genes are induced upon growth of S. meliloti on trans-4-l-Hyp, and of those, hypMNPQ encodes an ABC-type trans-4-l-Hyp transporter and hypRE encodes an epimerase that converts trans-4-l-Hyp to cis-4-d-Hyp in the bacterial cytoplasm. Here, we present evidence that the HypO, HypD, and HypH proteins catalyze the remaining steps in which cis-4-d-Hyp is converted to α-ketoglutarate. The HypO protein functions as a d-amino acid dehydrogenase, converting cis-4-d-Hyp to Δ(1)-pyrroline-4-hydroxy-2-carboxylate, which is deaminated by HypD to α-ketoglutarate semialdehyde and then converted to α-ketoglutarate by HypH. The crystal structure of HypD revealed it to be a member of the N-acetylneuraminate lyase subfamily of the (α/β)8 protein family and is consistent with the known enzymatic mechanism for other members of the group. It was also shown that S. meliloti can catabolize d-proline as both a carbon and a nitrogen source, that d-proline can complement l-proline auxotrophy, and that the catabolism of d-proline is dependent on the hyp cluster. Transport of d-proline involves the HypMNPQ transporter, following which d-proline is converted to Δ(1)-pyrroline-2-carboxylate (P2C) largely via HypO. The P2C is converted to l-proline through the NADPH-dependent reduction of P2C by the previously uncharacterized HypS protein. Thus, overall, we have now completed detailed genetic and/or biochemical characterization of 9 of the 14 hyp genes.

PubMed: 26833407
DOI: 10.1128/JB.00961-15

Experimental method

X-RAY DIFFRACTION (1.92 Å)