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PDBsum entry 4kqm

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protein ligands Protein-protein interface(s) links
Transferase PDB id
4kqm
Jmol
Contents
Protein chains
638 a.a.
Ligands
UDP ×4
G6P ×4
PEG ×4
GLC-BGC
PDB id:
4kqm
Name: Transferase
Title: Crystal structure of yeast glycogen synthase e169q mutant in with glucose and udp
Structure: Gsy2p. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 764101. Strain: strain atcc 204508 / s288c. Gene: fosterso_3265, gsy2 ylr258w l8479.8. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.77Å     R-factor:   0.203     R-free:   0.241
Authors: V.M.Chikwana,T.D.Hurley
Key ref: V.M.Chikwana et al. (2013). Structural basis for 2'-phosphate incorporation into glycogen by glycogen synthase. Proc Natl Acad Sci U S A, 110, 20976-20981. PubMed id: 24324135 DOI: 10.1073/pnas.1310106111
Date:
15-May-13     Release date:   11-Dec-13    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P27472  (GYS2_YEAST) -  Glycogen [starch] synthase isoform 2
Seq:
Struc:
 
Seq:
Struc:
705 a.a.
638 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.11  - Glycogen(starch) synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glycogen
      Reaction: UDP-alpha-D-glucose + ((1->4)-alpha-D-glucosyl)(n) = UDP + ((1->4)-alpha- D-glucosyl)(n+1)
UDP-alpha-D-glucose
+ ((1->4)-alpha-D-glucosyl)(n)
=
UDP
Bound ligand (Het Group name = UDP)
corresponds exactly
+ ((1->4)-alpha- D-glucosyl)(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.1310106111 Proc Natl Acad Sci U S A 110:20976-20981 (2013)
PubMed id: 24324135  
 
 
Structural basis for 2'-phosphate incorporation into glycogen by glycogen synthase.
V.M.Chikwana, M.Khanna, S.Baskaran, V.S.Tagliabracci, C.J.Contreras, A.DePaoli-Roach, P.J.Roach, T.D.Hurley.
 
  ABSTRACT  
 
Glycogen is a glucose polymer that contains minor amounts of covalently attached phosphate. Hyperphosphorylation is deleterious to glycogen structure and can lead to Lafora disease. Recently, it was demonstrated that glycogen synthase catalyzes glucose-phosphate transfer in addition to its characteristic glucose transfer reaction. Glucose-1,2-cyclic-phosphate (GCP) was proposed to be formed from UDP-Glc breakdown and subsequently transferred, thus providing a source of phosphate found in glycogen. To gain further insight into the molecular basis for glucose-phosphate transfer, two structures of yeast glycogen synthase were determined; a 3.0-Å resolution structure of the complex with UMP/GCP and a 2.8-Å resolution structure of the complex with UDP/glucose. Structural superposition of the complexes revealed that the bound ligands and most active site residues are positioned similarly, consistent with the use of a common transfer mechanism for both reactions. The N-terminal domain of the UDP⋅glucose complex was found to be 13.3° more closed compared with a UDP complex. However, the UMP⋅GCP complex was 4.8° less closed than the glucose complex, which may explain the low efficiency of GCP transfer. Modeling of either α- or β-glucose or a mixture of both anomers can account for the observed electron density of the UDP⋅glucose complex. NMR studies of UDP-Glc hydrolysis by yeast glycogen synthase were used to verify the stereochemistry of the product, and they also showed synchronous GCP accumulation. The similarities in the active sites of glycogen synthase and glycogen phosphorylase support the idea of a common catalytic mechanism in GT-B enzymes independent of the specific reaction catalyzed.