PDBsum entry 2bwp

Transferase

PDB id: 2bwp

Contents

Protein chains

398 a.a. *

Ligands

PLG ×4

ACY ×3

Waters ×118

* Residue conservation analysis

PDB id:

2bwp

Name:

Transferase

Title:

5-aminolevulinate synthase from rhodobacter capsulatus in complex with glycine

Structure:

5-aminolevulinate synthase. Chain: a, b, d, e. Synonym: 5-aminolevulinic acid synthase, delta- aminolevulinate synthase, delta-ala synthetase. Engineered: yes

Source:

Rhodobacter capsulatus. Organism_taxid: 1061. Atcc: 11166. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: german collection of microorganisms (dsm) dsm 1710

Biol. unit:

Dimer (from PDB file)

Resolution:

2.70Å R-factor: 0.169 R-free: 0.220

Authors:

I.Astner,J.O.Schulze,J.J.Van Den Heuvel,D.Jahn,W.-D.Schubert, D.W.Heinz

Key ref:

I.Astner et al. (2005). Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans. EMBO J, 24, 3166-3177. PubMed id: 16121195 DOI: 10.1038/sj.emboj.7600792

Date:

15-Jul-05 Release date: 27-Sep-05

Protein chains

P18079  (HEM1_RHOCB) -  5-aminolevulinate synthase from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

Seq: 409 a.a.

Struc: 398 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.1.37 - 5-aminolevulinate synthase.
• Pathway: Porphyrin Biosynthesis (early stages)
• Reaction: succinyl-CoA + glycine + H⁺ = 5-aminolevulinate + CO2 + CoA

succinyl-CoA (Bound ligand (Het Group name = ACY) matches with 80.00% similarity) + glycine + H(+) = 5-aminolevulinate + CO2 + CoA

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLG) matches with 71.43% similarity)

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

reference

DOI no: 10.1038/sj.emboj.7600792

EMBO J 24:3166-3177 (2005)

PubMed id: 16121195

Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans.

I.Astner, J.O.Schulze, J.van den Heuvel, D.Jahn, W.D.Schubert, D.W.Heinz.

ABSTRACT

5-Aminolevulinate synthase (ALAS) is the first and rate-limiting enzyme of heme biosynthesis in humans, animals, other non-plant eukaryotes, and alpha-proteobacteria. It catalyzes the synthesis of 5-aminolevulinic acid, the first common precursor of all tetrapyrroles, from glycine and succinyl-coenzyme A (sCoA) in a pyridoxal 5'-phosphate (PLP)-dependent manner. X-linked sideroblastic anemias (XLSAs), a group of severe disorders in humans characterized by inadequate formation of heme in erythroblast mitochondria, are caused by mutations in the gene for erythroid eALAS, one of two human genes for ALAS. We present the first crystal structure of homodimeric ALAS from Rhodobacter capsulatus (ALAS(Rc)) binding its cofactor PLP. We, furthermore, present structures of ALAS(Rc) in complex with the substrates glycine or sCoA. The sequence identity of ALAS from R. capsulatus and human eALAS is 49%. XLSA-causing mutations may thus be mapped, revealing the molecular basis of XLSA in humans. Mutations are found to obstruct substrate binding, disrupt the dimer interface, or hamper the correct folding. The structure of ALAS completes the structural analysis of enzymes in heme biosynthesis.

Selected figure(s)

Figure 2.
Figure 2 Schematic representation of the active site. Glycine-bound PLP and sCoA are highlighted by bonds in black; bonds of surrounding residues are shown in dark orange. Dotted lines indicate hydrogen bonds (green numbers) and salt bridges (red) between substrates or cofactors and ALAS; green semicircles indicate hydrophobic interactions. An asterisk marks residues from the second monomer. Lys248, involved in PLP binding and catalysis, is marked by a blue box, residues affected by mutations in human eALAS by a red box.

Figure 6.
Figure 6 The reaction mechanism of ALAS. In the substrate-free state, the cofactor PLP is bound by Lys248 (ALAS[Rc]), the internal aldimine. Incoming glycine induces transaldimination, leading to PLP binding glycine rather than Lys248 (external aldimine). The substrate sCoA is nucleophilically attacked by the PLP-activated glycine, leading to the addition of succinic acid to glycine and concomitant loss of CoA. Decarboxylation (carboxylate of the glycine moiety) of this intermediate yields the PLP-bound product, released in the rate-limiting step of the reaction.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2005, 24, 3166-3177) copyright 2005.

Figures were selected by the author.

Author's comment

Tetrapyrroles, such as hemes and chlorophylls are arguably among the most important pigments in the biosphere and the most versatile of cofactors.
The initial and rate-limiting enzyme of tetrapyrrole biosynthesis 5-aminolevulinate synthase (ALAS; E.C. 2.3.1.37) was discovered by Shemin and Neuberger in the late 1950's. ALAS catalyzes the PLP-dependent decarboxylative condensation of glycine and succinyl-coenzyme A. The product aminolevulinic acid (ALA) is the universal precursor of all tetrapyrroles.
Much later, ALAS was found to be restricted to non-plant eukaryotes and the gamma-group of proteobacteria. In plants and most bacteria, ALA is instead derived from tRNA-bound glutamate in two enzymatic steps via the C5-pathway involving glutamyl-tRNA reductase and glutamate-1-semialdehyde-2,1-aminomutase (GSAM). The originally discovered biosynthesis is known as the "Shemin pathway".
X-linked sideroblastic anemias (XLSA) are a group of severe disorders in humans, characterized by inadequate formation of heme in erythroblast mitochondria. They are caused by mutations in the gene for erythroid eALAS, one of two human genes for human ALAS.
The structure 2bwn is the first crystal structure ALAS. It is the homodimeric ALAS from the purple bacterium Rhodobacter capsulatus (ALAS-Rc) and includes the cofactor pyridoxal 5�-phosphate (PLP). 2bwo and 2bwp, respectively, are structures of ALAS-Rc in complex with the substrates glycine or succinyl-CoA. By combining the two, the active site immediately prior to the ensuing enzymatic reaction may be derived.
The sequence identity of ALAS from R. capsulatus and human eALAS is 49%. XLSA-causing mutations can therefore be mapped onto the bacterial protein to reveal the molecular basis of XLSA in humans. Mutations are mainly found to obstruct substrate binding, disrupt the dimer interface, or hamper the correct folding.
Wolf-Dieter Schubert