Crystal structure of DmdD E121A in complex with MMPA-CoA

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA.

Tan, D.Crabb, W.M.Whitman, W.B.Tong, L.

(2013) PLoS One 8: e63870-e63870

  • DOI: https://doi.org/10.1371/journal.pone.0063870
  • Primary Citation of Related Structures:  
    4IZB, 4IZC, 4IZD

  • PubMed Abstract: 

    Dimethyl-sulphoniopropionate (DMSP) is produced in abundance by marine phytoplankton, and the catabolism of this compound is an important source of carbon and reduced sulfur for marine bacteria and other organisms. The enzyme DmdD catalyzes the last step in the methanethiol (MeSH) pathway of DMSP catabolism. DmdD is a member of the crotonase superfamily of enzymes, and it catalyzes both the hydration and the hydrolysis of methylthioacryloyl-CoA (MTA-CoA), converting it to acetaldehyde, CO2, MeSH, and CoA. We report here the crystal structure of Ruegeria pomeroyi DmdD free enzyme at 1.5 Å resolution and the structures of the E121A mutant in complex with MTA-CoA and 3-methylmercaptopropionate-CoA (MMPA-CoA) at 1.8 Å resolution. DmdD is a hexamer, composed of a dimer of trimers where the three monomers of each trimer are related by a crystallographic 3-fold axis. The overall structure of this hexamer is similar to those of canonical crotonases. However, the C-terminal loops of DmdD in one of the trimers assume a different conformation and contribute to CoA binding in the active site of a neighboring monomer of the trimer, while these loops in the second trimer are disordered. MTA-CoA is bound deep in the active site in the first trimer, but shows a 1.5 Å shift in its position in the second trimer. MMPA-CoA has a similar binding mode to MTA-CoA in the first trimer. MMPA-CoA cannot be hydrated and is only hydrolyzed slowly by DmdD. Replacement of the sulfur atom in MMPA-CoA with a methylene group abolishes hydrolysis, suggesting that the unique property of the substrate is a major determinant of the hydrolysis activity of DmdD.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase/isomerase family protein
A, B
275Ruegeria pomeroyi DSS-3Mutation(s): 1 
Gene Names: dmdD
Find proteins for Q5LLW6 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore Q5LLW6 
Go to UniProtKB:  Q5LLW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LLW6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1HE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-methylmercaptopropionate-CoA (MMPA-CoA)
C25 H42 N7 O17 P3 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.13α = 90
b = 117.13β = 90
c = 117.13γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release