1gtk Summary

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Time-resolved and static-ensemble structural studies of hydroxymethylbilane synthase

The structure was published by Helliwell, J.R., Nieh, Y.P., Habash, J., et al., Cianci, M., Wulff, M., and Hadener, A., in 2003 in a paper entitled "Time-Resolved and Static-Ensemble Structural Chemistry of Hydroxymethylbilane Synthase" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.66 Å and deposited in 2002.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of PORPHOBILINOGEN DEAMINASE. This molecule has the UniProt identifier P06983 (HEM3_ECOLI)search. The sample contained 313 residues which is 100% of the natural sequence. Out of 313 residues 292 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A PORPHOBILINOGEN DEAMINASE P06983 (1-313) (HEM3_ECOLI)search Escherichia coli K-12search 100% 313 93%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P06983 (1 - 313) PORPHOBILINOGEN DEAMINASE Escherichia coli

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A (P06983) Phosphate binding protein-likesearch, Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domainsearch Periplasmic binding protein-like IIsearch, Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domainsearch PF01379: Porphobilinogen deaminase, dipyromethane cofactor binding domainsearch, PF03900: Porphobilinogen deaminase, C-terminal domainsearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
A (P06983) tetrapyrrole biosynthetic processsearch peptidyl-pyrromethane cofactor linkagesearch heme biosynthetic processsearch protoporphyrinogen IX biosynthetic processsearch porphyrin-containing compound biosynthetic processsearch hydroxymethylbilane synthase activitysearch transferase activitysearch cytoplasmsearch

Chain InterPro annotation
A Tetrapyrrole biosynthesis, hydroxymethylbilane synthasesearch Porphobilinogen deaminase, N-terminalsearch Porphobilinogen deaminase, C-terminalsearch Porphobilinogen deaminase, dipyrromethane cofactor binding sitesearch