› 6oz6

X-ray diffraction
3.7Å resolution

Crystal structure of MraY bound to 3'-hydroxymureidomycin A

Released:
DOI: 10.2210/pdb6oz6/pdb
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PDB entry 6oz6 coloured by chain, front view.
PDB entry 6oz6 coloured by chain, side view.
PDB entry 6oz6 coloured by chain, top view.
Source organisms:
Primary publication:
Chemical logic of MraY inhibition by antibacterial nucleoside natural products.
Mashalidis EH, Kaeser B, Terasawa Y, Katsuyama A, Kwon DY, Lee K, Hong J, Ichikawa S, Lee SY
OpenAccess logo Nat Commun 10 2917 (2019)
PMID: 31266949

Function and Biology Details

Reaction catalysed: 
UDP-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate = UMP + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231671 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
MraYAA nanobody Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 137 amino acids
Theoretical weight: 15.06 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Phospho-N-acetylmuramoyl-pentapeptide-transferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 365 amino acids
Theoretical weight: 40.95 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O66465 (Residues: 1-359; Coverage: 100%)
Gene names: aq_053, mraY
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand NKD 3 x NKD
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 94.879Å b: 129.979Å c: 130.156Å
α: 90° β: 109.38° γ: 90°
R-values:
R R work R free
0.258 0.256 0.301
Expression system: Escherichia coli

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Citations

8 review citations

β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium.
Fisher et al. (2021)
7 more

2 mentions without citation

Structures of Bacterial MraY and Human GPT Provide Insights into Rational Antibiotic Design.
Mashalidis et al. (2020)
1 more

PDB-REDO

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