PDBsum entry 1l6y

Lyase

PDB id: 1l6y

Contents

Protein chains

323 a.a. *

Ligands

4OX ×2

GOL ×5

Metals

_ZN ×2

_MG ×2

Waters ×431

* Residue conservation analysis

PDB id:

1l6y

Name:

Lyase

Title:

Crystal structure of porphobilinogen synthase complexed with the inhibitor 4-oxosebacic acid

Structure:

Porphobilinogen synthase. Chain: a, b. Synonym: delta-aminolevulinic acid dehydratase, 5-aminolevulinic acid dehydratase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Octamer (from PDB file)

Resolution:

1.90Å R-factor: 0.206 R-free: 0.263

Authors:

E.K.Jaffe,J.Kervinen,J.Martins,F.Stauffer,R.Neier,A.Wlodawer,A.Zdanov

Key ref:

E.K.Jaffe et al. (2002). Species-specific inhibition of porphobilinogen synthase by 4-oxosebacic acid. J Biol Chem, 277, 19792-19799. PubMed id: 11909869 DOI: 10.1074/jbc.M201486200

Date:

14-Mar-02 Release date: 17-Apr-02

Protein chains

P0ACB2  (HEM2_ECOLI) -  Delta-aminolevulinic acid dehydratase from Escherichia coli (strain K12)

Seq: 324 a.a.

Struc: 323 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.2.1.24 - porphobilinogen synthase.
• Pathway: Porphyrin Biosynthesis (early stages)
• Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O + H⁺

2 × 5-aminolevulinate (Bound ligand (Het Group name = 4OX) matches with 43.75% similarity) = porphobilinogen + 2 × H2O + H(+)

• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M201486200

J Biol Chem 277:19792-19799 (2002)

PubMed id: 11909869

Species-specific inhibition of porphobilinogen synthase by 4-oxosebacic acid.

E.K.Jaffe, J.Kervinen, J.Martins, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov.

ABSTRACT

Porphobilinogen synthase (PBGS) catalyzes the condensation of two molecules of 5-aminolevulinic acid (ALA), an essential step in tetrapyrrole biosynthesis. 4-Oxosebacic acid (4-OSA) and 4,7-dioxosebacic acid (4,7-DOSA) are bisubstrate reaction intermediate analogs for PBGS. We show that 4-OSA is an active site-directed irreversible inhibitor for Escherichia coli PBGS, whereas human, pea, Pseudomonas aeruginosa, and Bradyrhizobium japonicum PBGS are insensitive to inhibition by 4-OSA. Some variants of human PBGS (engineered to resemble E. coli PBGS) have increased sensitivity to inactivation by 4-OSA, suggesting a structural basis for the specificity. The specificity of 4-OSA as a PBGS inhibitor is significantly narrower than that of 4,7-DOSA. Comparison of the crystal structures for E. coli PBGS inactivated by 4-OSA versus 4,7-DOSA shows significant variation in the half of the inhibitor that mimics the second substrate molecule (A-side ALA). Compensatory changes occur in the structure of the active site lid, which suggests that similar changes normally occur to accommodate numerous hybridization changes that must occur at C3 of A-side ALA during the PBGS-catalyzed reaction. A comparison of these with other PBGS structures identifies highly conserved active site water molecules, which are isolated from bulk solvent and implicated as proton acceptors in the PBGS-catalyzed reaction.

Selected figure(s)

Figure 4.
Fig. 4. A stereo diagram of the 4-OSA inactivated E. coli PBGS dimer. The two monomers are shown in blue and magenta, Zn2+ is dark green, Mg2+ is orange, and the active site lid is yellow. The two active site lysine residues are shown (ball-and-stick) with bonds colored according to the subunit; Lys246 makes Schiff base to atom C4 of the inhibitor. The 4-OSA molecules are shown (ball-and-stick) with bonds in green. Atom color code is C, green; N, blue; O, red.

Figure 6.
Fig. 6. Schematic diagram of the hydrogen bonding of 4-OSA (A) and 4,7-DOSA (B) with E. coli PBGS. The carbon atoms of 4-OSA and 4,7-DOSA are numbered. Water molecules are represented by single oxygen atoms as O. Dashed lines indicate potential hydrogen bonds using a heteroatom distance of 3.2 Å. Hydrogen bonds are depicted for subunits A. In subunit B the Gly213(O)-Arg204(N), the 4-OSA(O)-Arg204(NE), and the 4-OSA(O)-water(connected to Gln219) distances are 3.5-3.8 Å. Dotted lines indicate the Zn2+ ligand bonds, which are each ~2.4 Å.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 19792-19799) copyright 2002.

Figures were selected by an automated process.