PDBsum entry 1abb

Glycogen phosphorylase

PDB id: 1abb

Contents

Protein chains

824 a.a. *

Ligands

SO4 ×4

PDP ×4

IMP ×4

* Residue conservation analysis

PDB id:

1abb

Name:

Glycogen phosphorylase

Title:

Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on r-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate

Structure:

Glycogen phosphorylase b. Chain: a, b, c, d. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.210

Authors:

D.D.Leonidas,N.G.Oikonomakos,A.C.Papageorgiou,K.R.Acharya,D.Barford, L.N.Johnson

Key ref:

D.D.Leonidas et al. (1992). Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate. Protein Sci, 1, 1112-1122. PubMed id: 1304390 DOI: 10.1002/pro.5560010905

Date:

09-Apr-92 Release date: 31-Oct-93

Protein chains

P00489  (PYGM_RABIT) -  Glycogen phosphorylase, muscle form from Oryctolagus cuniculus

Seq: 843 a.a.

Struc: 824 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.4.1.1 - glycogen phosphorylase.
• Pathway: Glycogen
• Reaction: [(1->4)-alpha-D-glucosyl](n) + phosphate = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate

[(1->4)-alpha-D-glucosyl](n) + phosphate = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate (Bound ligand (Het Group name = IMP) matches with 50.00% similarity)

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

Added reference

DOI no: 10.1002/pro.5560010905

Protein Sci 1:1112-1122 (1992)

PubMed id: 1304390

Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate.

D.D.Leonidas, N.G.Oikonomakos, A.C.Papageorgiou, K.R.Acharya, D.Barford, L.N.Johnson.

ABSTRACT

Previous crystallographic studies on glycogen phosphorylase have described the different conformational states of the protein (T and R) that represent the allosteric transition and have shown how the properties of the 5'-phosphate group of the cofactor pyridoxal phosphate are influenced by these conformational states. The present work reports a study on glycogen phosphorylase b (GPb) complexed with a modified cofactor, pyridoxal 5'-diphosphate (PLPP), in place of the natural cofactor. Solution studies (Withers, S.G., Madsen, N.B., & Sykes, B.D., 1982, Biochemistry 21, 6716-6722) have shown that PLPP promotes R-state properties of the enzyme indicating that the cofactor can influence the conformational state of the protein. GPb complexed with pyridoxal 5'-diphosphate (PLPP) has been crystallized in the presence of IMP and ammonium sulfate in the monoclinic R-state crystal form and the structure refined from X-ray data to 2.8 A resolution to a crystallographic R value of 0.21. The global tertiary and quaternary structure in the vicinity of the Ser 14 and the IMP sites are nearly identical to those observed for the R-state GPb-AMP complex. At the catalytic site the second phosphate of PLPP is accommodated with essentially no change in structure from the R-state structure and is involved in interactions with the side chains of two lysine residues (Lys 568 and Lys 574) and the main chain nitrogen of Arg 569. Superposition of the T-state structure shows that were the PLPP to be incorporated into the T-state structure there would be a close contact with the 280s loop (residues 282-285) that would encourage the T to R allosteric transition. The second phosphate of the PLPP occupies a site that is distinct from other dianionic binding sites that have been observed for glucose-1-phosphate and sulfate (in the R state) and for heptulose-2-phosphate (in the T state). The results indicate mobility in the dianion recognition site, and the precise position is dependent on other linkages to the dianion. In the modified cofactor the second phosphate site is constrained by the covalent link to the first phosphate of PLPP. The observed position in the crystal suggests that it is too far from the substrate site to represent a site for catalysis.

Selected figure(s)

Figure 2.
ig. 2. Contacts to thepyrophosphate moiety of LPP or (A) sub- unit and (B) subunit 2. PLPPand rg 569 are shown as solid lines. n subunit 2 Arg 569 has shifted from its position in native R-state GPb nd makes acontactthrough its side chain tothe second phosphate of PLP.

Figure 4.
Fig. 4. Dianionbinding sites atthecatalytic site of GPb. Thediagram showsthepositionsof PLPP(presentwork)andthepositions of Lys 568, Arg 569, and Lys 574 asobserved in R-state Pb.Sulfate (Barford & Johnson, 1989) and glucose-1-P (Hu, 1991) positionsob- tainedfromstudieswiththeR-statecrystalsareshownassolidcircles. Hptulose-2-P,obtainedfromstudieswiththeT-satecrystals(Jhn- sonetal., 1990), s shownsuperimposedontheR-statestructure.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1992, 1, 1112-1122) copyright 1992.

Figures were selected by an automated process.