4J1O

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)

Summary for 4J1O

• Entry DOI: 10.2210/pdb4j1o/pdb
• Descriptor: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein, MAGNESIUM ION, IODIDE ION, ... (6 entities in total)
• Functional Keywords: enolase, betaine racemase, proline betaine racemease, nysgrc, structural genomics, new york structural genomics research consortium, psi-biology, isomerase
• Biological source: Paracoccus denitrificans
• Total number of polymer chains: 2
• Total formula weight: 85867.32

Authors

Vetting, M.W.,Toro, R.,Bhosle, R.,Wasserman, S.R.,Morisco, L.L.,Sojitra, S.,Chamala, S.,Kar, A.,LaFleur, J.,Villigas, G.,Evans, B.,Hammonds, J.,Gizzi, A.,Stead, M.,Hillerich, B.,Love, J.,Seidel, R.D.,Bonanno, J.B.,Gerlt, J.A.,Almo, S.C.,New York Structural Genomics Research Consortium (NYSGRC) (deposition date: 2013-02-01, release date: 2013-03-06, Last modification date: 2024-02-28)

Primary citation

Kumar, R.,Zhao, S.,Vetting, M.W.,Wood, B.M.,Sakai, A.,Cho, K.,Solbiati, J.,Almo, S.C.,Sweedler, J.V.,Jacobson, M.P.,Gerlt, J.A.,Cronan, J.E.
Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
MBio, 5:e00933-e00913, 2014

PubMed Abstract: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine.

PubMed: 24520058
DOI: 10.1128/mBio.00933-13

Experimental method

X-RAY DIFFRACTION (1.6 Å)