5VJ1

Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MdcA AI554Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: mdcAPA0208
Find proteins for Q9I6T0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
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Go to UniProtKB:  Q9I6T0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MdcC CK99Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: mdcCPFL_5818
Find proteins for Q4K4F7 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Explore Q4K4F7 
Go to UniProtKB:  Q4K4F7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MdcD DL287Pseudomonas aeruginosaMutation(s): 0 
Gene Names: madCmdcDAO964_31600AOY09_06294BH593_13640PAERUG_E15_London_28_01_14_07061PAERUG_P32_London_17_VIM_2_10_11_04127PAMH19_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
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MdcE EM284Pseudomonas aeruginosaMutation(s): 0 
Gene Names: madDAO964_31595AOY09_06293PAERUG_E15_London_28_01_14_07062PAERUG_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))
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Go to UniProtKB:  Q9I6S6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
D, L
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.74α = 90
b = 163.56β = 94.01
c = 100.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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