5VIT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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, havi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MdcA
A, I, P, V
554Pseudomonas 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))
Go to UniProtKB:  Q9I6T0

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MdcC
C, K, R, X
99Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: mdcCPFL_5818
Find proteins for Q4K4F7 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Go to UniProtKB:  Q4K4F7

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MdcD
D, L, S, Y
287Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
EC: 2.1.3.10 (PDB Primary Data), 2.1.3.1 (PDB Primary Data)
Find proteins for A0A071KS24 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A071KS24

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MdcE
E, M, T, Z
284Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
EC: 2.1.3.10 (PDB Primary Data), 4.1.1.88 (UniProt)
Find proteins for A0A0C6EV56 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A0C6EV56
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download CCD File 
A, I, P, V
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.51α = 90.8
b = 161.45β = 93.76
c = 102.72γ = 90.11
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