› 7cd0

X-ray diffraction
2.31Å resolution

Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human hydroxymethylbilane synthase

Released:
DOI: 10.2210/pdb7cd0/pdb
PDB entry 7cd0 coloured by chain, front view.
PDB entry 7cd0 coloured by chain, side view.
PDB entry 7cd0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Sato H, Sugishima M, Tsukaguchi M, Masuko T, Iijima M, Takano M, Omata Y, Hirabayashi K, Wada K, Hisaeda Y, Yamamoto K
Biochem J 478 1023-1042 (2021)
PMID: 33600566

Function and Biology Details

Reaction catalysed: 
4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140114 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Porphobilinogen deaminase Chains: A, B
Molecule details ›
Chains: A, B
Length: 361 amino acids
Theoretical weight: 39.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P08397 (Residues: 1-361; Coverage: 100%)
Gene names: HMBS, PBGD, UPS
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand 7J8 2 x 7J8
Ligand FWL 1 x FWL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 81.416Å b: 81.366Å c: 108.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.227 0.276
Expression system: Escherichia coli

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Citations

5 citation in other articles

Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies.
Helliwell JR. (2021)
4 more

2 mentions without citation

Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Sato et al. (2021)
1 more