5VIP

Crystal structure of Pseudomonas malonate decarboxylase MdcD-MdcE hetero-dimer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

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Literature

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.

Maderbocus, R., Fields, B.L., Hamilton, K., Luo, S., Tran, T.H., Dietrich, L.E.P., Tong, L.

(2017) Nat Commun 8: 160-160

  • DOI: 10.1038/s41467-017-00233-z
  • Primary Citation of Related Structures:  
    5VIP, 5VJ1, 5VIT

  • PubMed Abstract: 

    • Pseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having a ...

    Pseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Here we report the crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer, as well as biochemical and functional studies based on the structural information. We observe a malonate molecule in the active site of MdcA and we also determine the structure of malonate decarboxylase with CoA in the active site of MdcD-MdcE. Both structures provide molecular insights into malonate decarboxylase catalysis. Mutations in the hetero-tetramer interface can abolish holoenzyme formation. Mutations in the hetero-tetramer interface and the active sites can abolish Pseudomonas aeruginosa growth in a defined medium with malonate as the sole carbon source.Some aerobic bacteria contain a biotin-independent malonate decarboxylase (MDC), which allows them to use malonate as the sole carbon source. Here, the authors present the crystal structure of a Pseudomonas MDC and give insights into its catalytic mechanism and function.

    Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. ltong@columbia.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MdcE A, C284Pseudomonas aeruginosaMutation(s): 0 
Gene Names: madD, AO964_31595, AOY09_06293, PAERUG_E15_London_28_01_14_07062, PAERUG_P32_London_17_VIM_2_10_11_04128
EC: 2.1.3.10
Find proteins for Q9I6S6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I6S6 
Go to UniProtKB:  Q9I6S6
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MdcD B, D287Pseudomonas aeruginosaMutation(s): 0 
Gene Names: madC, mdcD, AO964_31600, AOY09_06294, BH593_13640, PAERUG_E15_London_28_01_14_07061, PAERUG_P32_London_17_VIM_2_10_11_04127, PAMH19_0209
EC: 2.1.3.10 (PDB Primary Data), 2.1.3.1 (PDB Primary Data)
Find proteins for Q9I6S7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I6S7 
Go to UniProtKB:  Q9I6S7
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.31α = 89.87
b = 60.076β = 88.77
c = 91.277γ = 68.8
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release