PDBsum entry 1z8d

Transferase

PDB id: 1z8d

Contents

Protein chain

821 a.a. *

Ligands

GLC

AMP

ADE

Waters ×369

* Residue conservation analysis

PDB id:

1z8d

Name:

Transferase

Title:

Crystal structure of human muscle glycogen phosphorylase a with amp and glucose

Structure:

Glycogen phosphorylase, muscle form. Chain: a. Synonym: myophosphorylase. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pygm. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.192 R-free: 0.251

Authors:

C.M.Lukacs,N.G.Oikonomakos,R.L.Crowther,L.N.Hong,R.U.Kammlott, W.Levin,S.Li,C.M.Liu,D.Lucas-Mcgady,S.Pietranico,L.Reik

Key ref:

C.M.Lukacs et al. (2006). The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: an intermediate conformation with T-state and R-state features. Proteins, 63, 1123-1126. PubMed id: 16523484 DOI: 10.1002/prot.20939

Date:

30-Mar-05 Release date: 21-Mar-06

Protein chain

P11217  (PYGM_HUMAN) -  Glycogen phosphorylase, muscle form from Homo sapiens

Seq: 842 a.a.

Struc: 821 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 = AMP) matches with 50.00% similarity)

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

Added reference

DOI no: 10.1002/prot.20939

Proteins 63:1123-1126 (2006)

PubMed id: 16523484

The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: an intermediate conformation with T-state and R-state features.

C.M.Lukacs, N.G.Oikonomakos, R.L.Crowther, L.N.Hong, R.U.Kammlott, W.Levin, S.Li, C.M.Liu, D.Lucas-McGady, S.Pietranico, L.Reik.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. (a) The overall fold of human muscle glycogen phosphorylase a. Because there was one molecule in the asymmetric unit, the active dimer was generated using a symmetry related molecule. Glucose, AMP, PLP, P-Ser 14, and adenine are shown and labeled. The positions of amino acids that differ between the human and rabbit muscle enzyme are shown in the blue monomer as yellow spheres. Figures were made with MOLSCRIPT[35] and Raster3D.[36] (b) Stereoview of the interactions between human muscle GPa and AMP. These interactions include extensive water-mediated contacts from the phosphate groups, several direct hydrogen bonds between the adenine and the AMP binding loop, and one hydrogen bond between the ribose and the cap region of the dimeric molecule. Van der Waals contacts from the adenine include an edge-to-face interaction with Phe 316 and a stacking interaction with Tyr 75. 2Fo-Fc density for the AMP is shown at 1 contour level. (c) Superposition of human muscle glycogen phosphorylase a (yellow) with human liver GPa with AMP bound (1FA9[6]) in orange and rabbit muscle GPb with AMP bound (7GPB[27]) in cyan, highlighting the difference in the allosteric site loop surrounding the AMP. Phe 316 is shown in for the viewer's clarification.

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 1123-1126) copyright 2006.