3U1T

Haloalkane Dehalogenase, DmmA, of marine microbial origin

• PDB DOI: https://doi.org/10.2210/pdb3U1T/pdb

• Classification: HYDROLASE
• Organism(s): unidentified
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-30 Released: 2011-12-28 
• Deposition Author(s): Gehret, J.J., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.177 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 

Literature

Structure and activity of DmmA, a marine haloalkane dehalogenase.

Gehret, J.J., Gu, L., Geders, T.W., Brown, W.C., Gerwick, L., Gerwick, W.H., Sherman, D.H., Smith, J.L.

(2012) Protein Sci 21: 239-248

• PubMed: 22124946 
• DOI: https://doi.org/10.1002/pro.2009
• Primary Citation of Related Structures:  
  3U1T


• PubMed Abstract: 
  

  DmmA is a haloalkane dehalogenase (HLD) identified and characterized from the metagenomic DNA of a marine microbial consortium. Dehalogenase activity was detected with 1,3-dibromopropane as substrate, with steady-state kinetic parameters typical of HLDs (K(m) = 0.24 ± 0.05 mM, k(cat) = 2.4 ± 0.1 s(-1) ). The 2.2-Å crystal structure of DmmA revealed a fold and active site similar to other HLDs, but with a substantially larger active site binding pocket, suggestive of an ability to act on bulky substrates. This enhanced cavity was shown to accept a range of linear and cyclic substrates, suggesting that DmmA will contribute to the expanding industrial applications of HLDs.

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Organizational Affiliation: 

Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.78 kDa 
• Atom Count: 5,164 
• Modelled Residue Count: 597 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DmmA Haloalkane Dehalogenase	A, B	309	unidentified	Mutation(s): 0  EC: 3.8.1.5
UniProt
Find proteins for Q6DND9 (Lyngbya majuscula) Explore Q6DND9  Go to UniProtKB:  Q6DND9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	E [auth A], H [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
CL	C [auth A], D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.177 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.784	α = 90
b = 99.784	β = 90
c = 122.004	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Gehret, J.J., Smith, J.L.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary