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Crystal structure of HypD, a 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Sinorhizobium meliloti
Structural highlights
FunctionPublication Abstract from PubMedSinorhizobium 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 alpha-ketoglutarate. The HypO protein functions as a D-amino acid dehydrogenase converting cis-4-D-Hyp to Delta1-pyrroline-4-hydroxy-2-carboxylate, which is deaminated by HypD to alpha-ketoglutarate semialdehyde and then converted to alpha-ketoglutarate by HypH. The crystal structure of HypD revealed it to be a member of the N-acetylneuraminate lyase sub-family of the (alpha/beta)8 protein family, and is consistent with the known enzymatic mechanism for other members of the group. It is also shown that S. meliloti can catabolize D-proline as both a carbon and nitrogen source, D-proline can complement L-proline auxotrophy, and that the catabolism of D-proline is dependent on the hyp cluster. Transport of D-proline involved the HypMNPQ transporter, and then its conversion to Delta1-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. IMPORTANCE: Hydroxyproline in proteins is abundant in animal and plant tissues, and serves as a carbon and nitrogen source for bacteria in diverse environments including the rhizosphere, compost, and mammalian gut. While the main biochemical features of bacterial hydroxyproline catabolism were elucidated in the 1960's, the genetic and molecular details are only recently being determined. Elucidating the genetics of hydroxyproline catabolism will aid the annotation of these genes in other genomes and metagenomic libraries. This will facilitate an improved understanding of the importance of this pathway, and may assist in determining the prevalence of hydroxyproline in a particular environment. L-Hydroxyproline and D-Proline Catabolism in Sinorhizobium meliloti.,Chen S, White CE, diCenzo GC, Zhang Y, Stogios PJ, Savchenko A, Finan TM J Bacteriol. 2016 Feb 1. pii: JB.00961-15. PMID:26833407[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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