PDBsum entry 2ptr

Lyase

PDB id: 2ptr

Contents

Protein chains

454 a.a. *

Ligands

2SA ×2

Waters ×610

* Residue conservation analysis

PDB id:

2ptr

Name:

Lyase

Title:

Crystal structure of escherichia coli adenylosuccinate lyase mutant h171a with bound adenylosuccinate substrate

Structure:

Adenylosuccinate lyase. Chain: a, b. Synonym: adenylosuccinate, asl. Engineered: yes. Mutation: yes

Source:

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

Resolution:

1.85Å R-factor: 0.183 R-free: 0.216

Authors:

M.Tsai,P.L.Howell

Key ref:

M.Tsai et al. (2007). Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism. J Mol Biol, 370, 541-554. PubMed id: 17531264 DOI: 10.1016/j.jmb.2007.04.052

Date:

08-May-07 Release date: 03-Jul-07

Protein chains

P0AB89  (PUR8_ECOLI) -  Adenylosuccinate lyase from Escherichia coli (strain K12)

Seq: 456 a.a.

Struc: 454 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.3.2.2 - adenylosuccinate lyase.
• Pathway: Purine Biosynthesis (late stages)
• Reaction:
  1. N₆-(1,2-dicarboxyethyl)-AMP = fumarate + AMP
  2. (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4- carboxamido]succinate = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4- carboxamide + fumarate

N(6)-(1,2-dicarboxyethyl)-AMP (Bound ligand (Het Group name = 2SA) corresponds exactly) = fumarate + AMP

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

reference

DOI no: 10.1016/j.jmb.2007.04.052

J Mol Biol 370:541-554 (2007)

PubMed id: 17531264

Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism.

M.Tsai, J.Koo, P.Yip, R.F.Colman, M.L.Segall, P.L.Howell.

ABSTRACT

Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5-aminoimidazole- (N-succinylocarboxamide) ribotide (SAICAR) to 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate, and of adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in the de novo purine biosynthetic pathway. ADL belongs to the argininosuccinate lyase (ASL)/fumarase C superfamily of enzymes. Members of this family share several common features including: a mainly alpha-helical, homotetrameric structure; three regions of highly conserved amino acid residues; and a general acid-base catalytic mechanism with the overall beta-elimination of fumarate as a product. The crystal structures of wild-type Escherichia coli ADL (ec-ADL), and mutant-substrate (H171A-ADS) and -product (H171N-AMP.FUM) complexes have been determined to 2.0, 1.85, and 2.0 A resolution, respectively. The H171A-ADS and H171N-AMP.FUM structures provide the first detailed picture of the ADL active site, and have enabled the precise identification of substrate binding and putative catalytic residues. Contrary to previous suggestions, the ec-ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec-ADL with other superfamily members suggest for the first time a large conformational movement of the flexible C3 loop (residues 287-303) in ec-ADL upon substrate binding and catalysis, resulting in its closure over the active site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the superimposed H171A (pink) and H171N (green) active sites, showing the interactions involving the AMP (a) and fumarate groups (c). The σ[A] weighted F[o]–F[c] omit maps for the substrate (orange) and products (blue) in the H171A and H171N proteins, respectively, are shown contoured at 3σ. Water molecules are shown as spheres. The corresponding schematic representations for the AMP and fumarate groups are shown in (b) and (d), respectively. Hydrogen bonds are represented as red broken lines with the distances indicated in angstroms (Å). Distances for the H171N protein are in bold, and the distances for active site 2 of each protein are given in parentheses. The letter following the residue number denotes the monomer to which each residue belongs, with those for active site 2 of the proteins shown in parentheses. In (b), residues involved in coordinating water molecules are colored blue. Poor electron density did not allow residues S295 and S296 in active site 2 of the H171A protein to be modeled. PyMol was used for Figure preparation.

Figure 3.
Figure 3. Stereo view of the superimposed H171A–ADS (pink), H171N–AMP•FUM (blue) and dδc1-SO[4]^2- (yellow) active sites, showing the conformation of the C3 loop in the proteins. Since the C3 loop in the SeMet protein could not be modeled due to the absence of electron density, the open conformation of the loop observed in the dδc2-S281A mutant^12 is also shown for comparison (green). The side-chains of selected C3 loop residues are shown and numbered according to the E. coli ADL sequence. PyMol was used for Figure preparation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 541-554) copyright 2007.

Figures were selected by an automated process.