› 5vit

X-ray diffraction
2.2Å resolution

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

Released:
DOI: 10.2210/pdb5vit/pdb
PDB entry 5vit coloured by chain, front view.
PDB entry 5vit coloured by chain, side view.
PDB entry 5vit coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.
Maderbocus R, Fields BL, Hamilton K, Luo S, Tran TH, Dietrich LEP, Tong L
Nat Commun 8 160 (2017)
PMID: 28757619

Function and Biology Details

Reactions catalysed: 
(S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate
A malonyl-[acyl-carrier protein] + a biotinyl-[protein] = an acetyl-[acyl-carrier protein] + a carboxybiotinyl-[protein]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero octamer
PDBe Complex ID:
PDB-CPX-175595 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Malonate decarboxylase alpha subunit Chains: A, I, P, V
Molecule details ›
Chains: A, I, P, V
Length: 554 amino acids
Theoretical weight: 61.5 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I6T0 (Residues: 1-554; Coverage: 100%)
Gene names: PA0208, mdcA
Sequence domains: Malonate decarboxylase, alpha subunit, transporter
Malonate decarboxylase acyl carrier protein Chains: C, K, R, X
Molecule details ›
Chains: C, K, R, X
Length: 99 amino acids
Theoretical weight: 10.69 KDa
Source organism: Pseudomonas protegens Pf-5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q4K4F7 (Residues: 1-99; Coverage: 100%)
Gene names: PFL_5818, mdcC
Sequence domains: Malonate decarboxylase delta subunit (MdcD)
CoA carboxyltransferase N-terminal domain-containing protein Chains: D, L, S, Y
Molecule details ›
Chains: D, L, S, Y
Length: 287 amino acids
Theoretical weight: 30.37 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I6S7 (Residues: 1-287; Coverage: 100%)
Gene names: PA0211, mdcD
Sequence domains: Carboxyl transferase domain
Malonate decarboxylase gamma subunit Chains: E, M, T, Z
Molecule details ›
Chains: E, M, T, Z
Length: 284 amino acids
Theoretical weight: 30.35 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I6S6 (Residues: 1-268; Coverage: 100%)
Gene names: PA0212, mdcE
Sequence domains: Malonate decarboxylase gamma subunit (MdcE)

Ligands and Environments

1 bound ligand:
Ligand MLI 4 x MLI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 93.51Å b: 161.45Å c: 102.72Å
α: 90.8° β: 93.76° γ: 90.11°
R-values:
R R work R free
0.188 0.186 0.232
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins.
Hackmann TJ. (2022)
3 more

1 mention without citation

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.
Maderbocus et al. (2017)