PDBsum entry: 1yp3

Transferase

PDB id: 1yp3

Contents

Protein chains

433 a.a. *

Ligands

SO4 ×13

ATP ×2

Waters ×254

* Residue conservation analysis

PDB id:

1yp3

Name:

Transferase

Title:

Crystal structure of potato tuber adp-glucose pyrophosphorylase in complex with atp

Structure:

Glucose-1-phosphate adenylyltransferase small subunit. Chain: a, b, c, d. Synonym: adp-glucose synthase, adp-glucose pyrophosphorylase, agpase b, alpha-d-glucose-1-phosphate adenyl transferase. Engineered: yes

Source:

Solanum tuberosum. Potato. Organism_taxid: 4113. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.175 R-free: 0.255

Authors:

X.Jin,M.A.Ballicora,J.Preiss,J.H.Geiger

Key ref:

X.Jin et al. (2005). Crystal structure of potato tuber ADP-glucose pyrophosphorylase. EMBO J, 24, 694-704. PubMed id: 15692569 DOI: 10.1038/sj.emboj.7600551

Date:

29-Jan-05 Release date: 15-Mar-05

Protein chains

P23509  (GLGS_SOLTU) -  Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic

Seq: 521 a.a.

Struc: 433 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.27 - Glucose-1-phosphate adenylyltransferase.
• Reaction: ATP + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose

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

 Gene Ontology (GO) functional annotation 

• Biological process: biosynthetic process (2 terms)
• Biochemical function: transferase activity (3 terms)

reference

DOI no: 10.1038/sj.emboj.7600551

EMBO J 24:694-704 (2005)

PubMed id: 15692569

Crystal structure of potato tuber ADP-glucose pyrophosphorylase.

X.Jin, M.A.Ballicora, J.Preiss, J.H.Geiger.

ABSTRACT

ADP-glucose pyrophosphorylase catalyzes the first committed and rate-limiting step in starch biosynthesis in plants and glycogen biosynthesis in bacteria. It is the enzymatic site for regulation of storage polysaccharide accumulation in plants and bacteria, being allosterically activated or inhibited by metabolites of energy flux. We report the first atomic resolution structure of ADP-glucose pyrophosphorylase. Crystals of potato tuber ADP-glucose pyrophosphorylase alpha subunit were grown in high concentrations of sulfate, resulting in the sulfate-bound, allosterically inhibited form of the enzyme. The N-terminal catalytic domain resembles a dinucleotide-binding Rossmann fold and the C-terminal domain adopts a left-handed parallel beta helix that is involved in cooperative allosteric regulation and a unique oligomerization. We also report structures of the enzyme in complex with ATP and ADP-glucose. Communication between the regulator-binding sites and the active site is both subtle and complex and involves several distinct regions of the enzyme including the N-terminus, the glucose-1-phosphate-binding site, and the ATP-binding site. These structures provide insights into the mechanism for catalysis and allosteric regulation of the enzyme.

Selected figure(s)

Figure 2.
Figure 2 (A) ADP-Glc PPase monomer. Yellow, catalytic domain; pink, -helix domain; ADP-Glc and sulfates are shown in atom type: carbon, green; oxygen, red; nitrogen, blue; phosphorous, magenta; sulfate, orange. (B) Overlay of ADP-Glc PPase (cyan), RmlA (r.m.s.d. 1.9 Å) (magenta), and GlmU (gold) (r.m.s.d. 2.5 Å). (C) ADP-Glc PPase tetramer. The disulfide bond between A and A' is boxed. (D) Interactions between monomers in the tetramer.

Figure 3.
Figure 3 (A) ADP-Glc PPase A subunit sulfate-binding region. A subunit, green ribbon; B subunit, purple ribbon; sulfates and interacting residues are colored by atom type. (B) Inhibition of potato tuber ADP-Glc PPase small subunit by sulfate.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 694-704) copyright 2005.

Figures were selected by an automated process.