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2.5.1.61: hydroxymethylbilane synthase

This is an abbreviated version!
For detailed information about hydroxymethylbilane synthase, go to the full flat file.

Word Map on EC 2.5.1.61

Reaction

4 porphobilinogen +

H2O
=
Hydroxymethylbilane
 + 4 NH3

Synonyms

(HMB)-synthase, AN0121.3, EC 4.3.1.8, HemC, hepatic porphobilinogen deaminase, HMB synthase, HMB-S, HMBS, HMBS1a-synthase, HMBS1b-synthase, HMBS2a-synthase, HMBS2b-synthase, human non-erythropoietic PBGD isoform, human PBGD, human porphobilinogen deaminase, hydroxymethylbilane synthase, More, PBG deaminase, PBG-D, PBG-deaminase, PBGD, PGB-D, porphobilinogen ammonia-lyase (polymerizing), porphobilinogen deaminase, pre-uroporphyrinogen synthase, preuroporphyrinogen synthase, preuroporphyrinogen synthetase, synthase, uroporphyrinogen I, uPBGD, UPGI-S, URO-S, urogenI synthase, uroporphyrinogen I synthase, uroporphyrinogen I synthetase, uroporphyrinogen synthase, uroporphyrinogen synthetase

ECTree

     2 Transferases
         2.5 Transferring alkyl or aryl groups, other than methyl groups
             2.5.1 Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)
                2.5.1.61 hydroxymethylbilane synthase

Crystallization

Crystallization on EC 2.5.1.61 - hydroxymethylbilane synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme with bound cofactor, crystallization in the dark due to light-sensitivity of the cofactor, hanging drop method, mixing of 5 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 5 mM DTT, with reservoir solution containing 25% w/v PEG 4000, 100 mM sodium citrate, pH 5.6, and 200 mM ammonium sulfate, X-ray diffraction structure determination and analysis at 1.45 A resolution, molecular modelling
SeMet-labelled enzyme
-
molecular dynamics simulations reveal that the HMBS active-site loop movement and cofactor turn create space for the elongating pyrrole chain. Twenty-seven residues around the active site and water molecules interact to stabilize the large, negatively charged, elongating polypyrrole. Residues R26 and R167 are the strongest candidates for proton transfer to deaminate the incoming porphobilinogen molecules. R167 is a gatekeeper and facilitator of hydroxymethylbilane egress through the space between the enzyme's domains and the active-site loop
network analysis identifies 13 structural clusters persistent across five molecular dynamics trajectories corresponding to the five steps of pyrrole polymerization, which are responsible for maintaining the tertiary structure and domain arrangements of the enzyme. Amino acid residues R26 and F77 regulate the active site loop movement across the stages
vapor diffusion method, hanging drops with 20 mM Tris-HCl buffer, pH 8.2, containing 5 mM dithiothreitol and reservoir solution consisting of 0.6 M ammonium sulfate, 1.2 M lithium sulfate, 5% ethylene glycol, 50 mM sodium citrate, pH 5.6, and 50 mM dithiothreitol, diffraction data are collected at -173°C in 30% glycerol cryoprotected protein crystals
purified recombinant detagged enzyme, mixing of 2.5 mg/ml protein with 0.1 M sodium cacodylate, pH 6.5-6.8, 0.2 M magnesium acetate, and 25-30%PEG 8000, room temperature, removal of the His tag is necessary to obtain enzyme crystals, X-ray diffraction structure determination and analysis at 1.46-1.60 A resolution
purified recombinant detagged enzyme, mixing of 2.5 mg/ml protein with 0.1 M sodium cacodylate, pH 6.5-6.8, 0.2 M magnesium acetate, and 25-30%PEG 8000, X-ray diffraction structure determination and analysis at 1.46-1.60 A resolution