PDBsum entry 1pv8

Lyase

PDB id: 1pv8

Contents

Protein chain

276 a.a. *

Ligands

PB1

Metals

_ZN ×2

Waters ×241

* Residue conservation analysis

PDB id:

1pv8

Name:

Lyase

Title:

Crystal structure of a low activity f12l mutant of human porphobilinogen synthase

Structure:

Delta-aminolevulinic acid dehydratase. Chain: a, b. Synonym: porphobilinogen synthase, aladh. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: alad. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.20Å R-factor: 0.199 R-free: 0.284

Authors:

S.Breinig,J.Kervinen,L.Stith,A.S.Wasson,R.Fairman,A.Wlodawer, A.Zdanov,E.K.Jaffe

Key ref:

S.Breinig et al. (2003). Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase. Nat Struct Biol, 10, 757-763. PubMed id: 12897770 DOI: 10.1038/nsb963

Date:

26-Jun-03 Release date: 09-Sep-03

Protein chains

P13716  (HEM2_HUMAN) -  Delta-aminolevulinic acid dehydratase from Homo sapiens

Seq: 330 a.a.

Struc: 276 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 = porphobilinogen (Bound ligand (Het Group name = PB1) corresponds exactly) + 2 × H2O + H(+)

• Cofactor: Zn(2+)

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

Added reference

DOI no: 10.1038/nsb963

Nat Struct Biol 10:757-763 (2003)

PubMed id: 12897770

Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase.

S.Breinig, J.Kervinen, L.Stith, A.S.Wasson, R.Fairman, A.Wlodawer, A.Zdanov, E.K.Jaffe.

ABSTRACT

Porphobilinogen synthase (PBGS) catalyzes the first common step in the biosynthesis of tetrapyrroles (such as heme and chlorophyll). Although the predominant oligomeric form of this enzyme, as inferred from many crystal structures, is that of a homo-octamer, a rare human PBGS allele, F12L, reveals the presence of a hexameric form. Rearrangement of an N-terminal arm is responsible for this oligomeric switch, which results in profound changes in kinetic behavior. The structural transition between octamer and hexamer must proceed through an unparalleled equilibrium containing two different dimer structures. The allosteric magnesium, present in most PBGS, has a binding site in the octamer but not in the hexamer. The unprecedented structural rearrangement reported here relates to the allosteric regulation of PBGS and suggests that alternative PBGS oligomers may function in a magnesium-dependent regulation of tetrapyrrole biosynthesis in plants and some bacteria.

Selected figure(s)

Figure 1.
Figure 1. Characteristics of wild-type human PBGS relative to the F12L variant. (a) The pH-rate profile for human PBGS ( ) exhibits a two-proton activating pK[a] of 5.9 and a one-proton deactivating pK[b] of 8.3. In contrast, the F12L variant ( ) shows a single one-proton activating pK[a] of 8.5. (b) The chromatographic separation of wild-type human (WT) PBGS and the F12L variant on a mono-Q column. (c) The differential mobility of wild-type (WT) human PBGS and the F12L variant on 12.5% (w/v) native PAGE.

Figure 3.
Figure 3. Characteristics of coexpressed WT+F12L. (a) Separation of two peaks of PBGS protein on Q-Sepharose; KCl gradient (red line), A(black line). Both pools showed PBGS activity at pH 7 ( ) and at pH 9 ( ). (b) The mobility of the two pools of WT+F12L relative to wild-type (WT) human PBGS and the F12L variant on native gel electrophoresis. (c) The pH-rate profiles for pool I ( ) and pool II ( ) after further purification on Sephacryl S300. (d) Determination of K[m] and V[max] values for the S300 purified pool I ( ) and pool II ( [280][glyph.gif] ) at pH 7 (black) and pH 9 (red). Dashed lines indicate the poor fits to standard hyperbolic saturation kinetics. Solid lines indicate the superior fit to a double hyperbola model where two forms of the enzyme are catalyzing the same reaction (see text and Table 1).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 757-763) copyright 2003.

Figures were selected by an automated process.