4B28

Crystal structure of DMSP lyase RdDddP from Roseobacter denitrificans

Summary for 4B28

• Entry DOI: 10.2210/pdb4b28/pdb
• Related: 4B28
• Descriptor: METALLOPEPTIDASE, FAMILY M24, PUTATIVE, FE (III) ION (3 entities in total)
• Functional Keywords: lyase, imethylsulfonioproionate, acrylate, dimethylsulfide
• Biological source: ROSEOBACTER DENITRIFICANS OCH 114
• Total number of polymer chains: 1
• Total formula weight: 53151.81

Authors

Hehemann, J.H.,Law, A.,Redecke, L.,Boraston, A.B. (deposition date: 2012-07-12, release date: 2012-07-25, Last modification date: 2024-05-08)

Primary citation

Hehemann, J.H.,Law, A.,Redecke, L.,Boraston, A.B.
The Structure of Rddddp from Roseobacter Denitrificans Reveals that Dmsp Lyases in the Dddp-Family are Metalloenzymes.
Plos One, 9:03128-, 2014

PubMed Abstract: Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 Å resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 Å apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes.

PubMed: 25054772
DOI: 10.1371/JOURNAL.PONE.0103128

Experimental method

X-RAY DIFFRACTION (2.15 Å)