spacer
spacer

PDBsum entry 1b4d
Go to PDB code: 
protein ligands links
Transferase PDB id
1b4d

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
804 a.a. *
Ligands
CRA
PLP
IMP
Waters ×820
* Residue conservation analysis
PDB id:
1b4d
Name: Transferase
Title: Amidocarbamate inhibitor of glycogen phosphorylase
Structure: Protein (glycogen phosphorylase b). Chain: a. Ec: 2.4.1.1
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: muscle
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.182     R-free:   0.229
Authors: K.E.Tsitsanou,N.G.Oikonomakos,S.E.Zographos,V.T.Skamnaki,M.Gregoriou, K.A.Watson,L.N.Johnson,G.W.J.Fleet
Key ref: K.E.Tsitsanou et al. (1999). Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure. Protein Sci, 8, 741-749. PubMed id: 10211820 DOI: 10.1110/ps.8.4.741
Date:
18-Dec-98     Release date:   23-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00489  (PYGM_RABIT) -  Glycogen phosphorylase, muscle form from Oryctolagus cuniculus
Seq:
Struc: 		 
Seq:
Struc: 		843 a.a.
804 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.1  - glycogen phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      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: 10.1110/ps.8.4.741 Protein Sci 8:741-749 (1999)
PubMed id: 10211820  
 
 
Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure.
K.E.Tsitsanou, N.G.Oikonomakos, S.E.Zographos, V.T.Skamnaki, M.Gregoriou, K.A.Watson, L.N.Johnson, G.W.Fleet.
 
  ABSTRACT  
 
The effects of a number of cryoprotectants on the kinetic and structural properties of glycogen phosphorylase b have been investigated. Kinetic studies showed that glycerol, one of the most commonly used cryoprotectants in X-ray crystallographic studies, is a competitive inhibitor with respect to substrate glucose-1-P with an apparent Ki value of 3.8% (v/v). Cryogenic experiments, with the enzyme, have shown that glycerol binds at the catalytic site and competes with glucose analogues that bind at the catalytic site, thus preventing the formation of complexes. This necessitated a change in the conditions for cryoprotection in crystallographic binding experiments with glycogen phosphorylase. It was found that 2-methyl-2,4-pentanediol (MPD), polyethylene glycols (PEGs) of various molecular weights, and dimethyl sulfoxide (DMSO) activated glycogen phosphorylase b to different extents, by stabilizing its most active conformation, while sucrose acted as a noncompetitive inhibitor and ethylene glycol as an uncompetitive inhibitor with respect to glucose-1-P. A parallel experimental investigation by X-ray crystallography showed that, at 100 K, both MPD and DMSO do not bind at the catalytic site, do not induce any significant conformational change on the enzyme molecule, and hence, are more suitable cryoprotectants than glycerol for binding studies with glycogen phosphorylase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
16266274 T.B.Eronina, N.A.Chebotareva, and B.I.Kurganov (2005).
Influence of osmolytes on inactivation and aggregation of muscle glycogen phosphorylase b by guanidine hydrochloride. Stimulation of protein aggregation under crowding conditions.
  Biochemistry (Mosc), 70, 1020-1026.  
14763976 F.Movahedzadeh, D.A.Smith, R.A.Norman, P.Dinadayala, J.Murray-Rust, D.G.Russell, S.L.Kendall, S.C.Rison, M.S.McAlister, G.J.Bancroft, N.Q.McDonald, M.Daffe, Y.Av-Gay, and N.G.Stoker (2004).
The Mycobacterium tuberculosis ino1 gene is essential for growth and virulence.
  Mol Microbiol, 51, 1003-1014.  
12454465 C.Charron, A.Kadri, M.C.Robert, R.Giegé, and B.Lorber (2002).
Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin.
  Acta Crystallogr D Biol Crystallogr, 58, 2060-2065.
PDB codes: 1lxz 1ly0
11717524 D.J.Derbyshire, D.J.Ellar, and J.Li (2001).
Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine.
  Acta Crystallogr D Biol Crystallogr, 57, 1938-1944.  
11168388 N.A.Chebotareva, S.E.Harding, and D.J.Winzor (2001).
Ultracentrifugal studies of the effect of molecular crowding by trimethylamine N-oxide on the self-association of muscle glycogen phosphorylase b.
  Eur J Biochem, 268, 506-513.  
10531512 E.Garman (1999).
Cool data: quantity AND quality.
  Acta Crystallogr D Biol Crystallogr, 55, 1641-1653.  
  10548038 N.G.Oikonomakos, K.E.Tsitsanou, S.E.Zographos, V.T.Skamnaki, S.Goldmann, and H.Bischoff (1999).
Allosteric inhibition of glycogen phosphorylase a by the potential antidiabetic drug 3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5,6-tricarbo xylate.
  Protein Sci, 8, 1930-1945.
PDB codes: 2gpa 3amv
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

spacer
spacer