› 2ybo

X-ray diffraction
2Å resolution

The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH

Released:
DOI: 10.2210/pdb2ybo/pdb
PDB entry 2ybo coloured by chain, front view.
PDB entry 2ybo coloured by chain, side view.
PDB entry 2ybo coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Crystal structure of the heme d1 biosynthesis enzyme NirE in complex with its substrate reveals new insights into the catalytic mechanism of S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferases.
Storbeck S, Saha S, Krausze J, Klink BU, Heinz DW, Layer G
J Biol Chem 286 26754-67 (2011)
PMID: 21632530

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + uroporphyrinogen III = S-adenosyl-L-homocysteine + precorrin-1
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161153 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
uroporphyrinogen-III C-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 294 amino acids
Theoretical weight: 31.4 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P95417 (Residues: 1-279; Coverage: 100%)
Gene names: DT376_23645, GUL26_18015, IPC1295_09180, PAERUG_P19_London_7_VIM_2_05_10_02002, cobA, cysG_1, nirE
Sequence domains: Tetrapyrrole (Corrin/Porphyrin) Methylases
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 60.9Å b: 115.1Å c: 76.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.235 0.287
Expression system: Escherichia coli BL21(DE3)

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Citations

5 review citations

Architectures, mechanisms and molecular evolution of natural product methyltransferases.
Liscombe et al. (2012)
4 more

2 mentions without citation

Crystal structure of the heme d1 biosynthesis enzyme NirE in complex with its substrate reveals new insights into the catalytic mechanism of S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferases.
Storbeck et al. (2011)
1 more