› 4mcw

X-ray diffraction
2.03Å resolution

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

Released:
DOI: 10.2210/pdb4mcw/pdb
PDB entry 4mcw coloured by chain, front view.
PDB entry 4mcw coloured by chain, side view.
PDB entry 4mcw coloured by chain, top view.
Source organism: Persephonella marina EX-H1
Primary publication:
Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre.
Bellini D, Caly DL, McCarthy Y, Bumann M, An SQ, Dow JM, Ryan RP, Walsh MA
Mol Microbiol 91 26-38 (2014)
PMID: 24176013

Function and Biology Details

Reaction catalysed: 
Hydrolytically removes 5'-nucleotides successively from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111033 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
HD-GYP domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 369 amino acids
Theoretical weight: 42.77 KDa
Source organism: Persephonella marina EX-H1
Expression system: Escherichia coli
UniProt:
  • Canonical: C0QQ26 (Residues: 2-363; Coverage: 100%)
Gene name: PERMA_0986
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand FE 6 x FE
Ligand SIN 6 x SIN
Ligand IMD 1 x IMD
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: I222
Unit cell:
a: 69.83Å b: 182.38Å c: 232.47Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.213
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Cyclic di-GMP: second messenger extraordinaire.
Jenal et al. (2017)
9 more

8 mentions without citation

Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases.
Galperin et al. (2022)
7 more