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PDBsum entry 1yp4

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1yp4
Jmol
Contents
Protein chains
432 a.a. *
Ligands
SO4 ×16
ADP ×2
ADQ
Waters ×471
* Residue conservation analysis
PDB id:
1yp4
Name: Transferase
Title: Crystal structure of potato tuber adp-glucose pyrophosphorylase in complex with adp-glucose
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:
2.30Å     R-factor:   0.183     R-free:   0.244
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23509  (GLGS_SOLTU) -  Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic
Seq:
Struc:
 
Seq:
Struc:
521 a.a.
432 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.27  - Glucose-1-phosphate adenylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose
ATP
Bound ligand (Het Group name = ADP)
matches with 87.00% similarity
+ alpha-D-glucose 1-phosphate
= diphosphate
+
ADP-glucose
Bound ligand (Het Group name = ADQ)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   2 terms 
  Biochemical function     nucleotidyltransferase activity     2 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 ) (magenta), and GlmU (gold) (r.m.s.d. 2.5 ). (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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20699404 C.Vriet, T.Welham, A.Brachmann, M.Pike, J.Pike, J.Perry, M.Parniske, S.Sato, S.Tabata, A.M.Smith, and T.L.Wang (2010).
A suite of Lotus japonicus starch mutants reveals both conserved and novel features of starch metabolism.
  Plant Physiol, 154, 643-655.  
20236089 M.Petreikov, M.Eisenstein, Y.Yeselson, J.Preiss, and A.A.Schaffer (2010).
Characterization of the AGPase large subunit isoforms from tomato indicates that the recombinant L3 subunit is active as a monomer.
  Biochem J, 428, 201-212.  
20482518 T.Yang, and M.Bar-Peled (2010).
Identification of a novel UDP-sugar pyrophosphorylase with a broad substrate specificity in Trypanosoma cruzi.
  Biochem J, 429, 533-543.  
20400541 Z.Zhang, J.Akutsu, and Y.Kawarabayasi (2010).
Identification of novel acetyltransferase activity on the thermostable protein ST0452 from Sulfolobus tokodaii strain 7.
  J Bacteriol, 192, 3287-3293.  
19876371 I.Baris, A.Tuncel, N.Ozber, O.Keskin, and I.H.Kavakli (2009).
Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase.
  PLoS Comput Biol, 5, e1000546.  
19737928 M.L.Kuhn, C.A.Falaschetti, and M.A.Ballicora (2009).
Ostreococcus tauri ADP-glucose pyrophosphorylase reveals alternative paths for the evolution of subunit roles.
  J Biol Chem, 284, 34092-34102.  
19505928 S.Comparot-Moss, and K.Denyer (2009).
The evolution of the starch biosynthetic pathway in cereals and other grasses.
  J Exp Bot, 60, 2481-2492.  
18641076 A.Tuncel, I.H.Kavakli, and O.Keskin (2008).
Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase.
  Biophys J, 95, 3628-3639.  
18700010 N.Georgelis, E.L.Braun, and L.C.Hannah (2008).
Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants.
  BMC Evol Biol, 8, 232.  
18199755 S.K.Hwang, Y.Nagai, D.Kim, and T.W.Okita (2008).
Direct appraisal of the potato tuber ADP-glucose pyrophosphorylase large subunit in enzyme function by study of a novel mutant form.
  J Biol Chem, 283, 6640-6647.  
17434970 D.Aragão, A.M.Fialho, A.R.Marques, E.P.Mitchell, I.Sá-Correia, and C.Frazão (2007).
The complex of Sphingomonas elodea ATCC 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members.
  J Bacteriol, 189, 4520-4528.
PDB code: 2ux8
17178129 J.G.McCoy, E.Bitto, C.A.Bingman, G.E.Wesenberg, R.M.Bannen, D.A.Kondrashov, and G.N.Phillips (2007).
Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP.
  J Mol Biol, 366, 830-841.
PDB codes: 1z90 2icx 2icy
17496097 M.A.Ballicora, E.D.Erben, T.Yazaki, A.L.Bertolo, A.M.Demonte, J.R.Schmidt, M.Aleanzi, C.M.Bejar, C.M.Figueroa, C.M.Fusari, A.A.Iglesias, and J.Preiss (2007).
Identification of regions critically affecting kinetics and allosteric regulation of the Escherichia coli ADP-glucose pyrophosphorylase by modeling and pentapeptide-scanning mutagenesis.
  J Bacteriol, 189, 5325-5333.  
17303565 T.Steiner, A.C.Lamerz, P.Hess, C.Breithaupt, S.Krapp, G.Bourenkov, R.Huber, R.Gerardy-Schahn, and U.Jacob (2007).
Open and closed structures of the UDP-glucose pyrophosphorylase from Leishmania major.
  J Biol Chem, 282, 13003-13010.
PDB codes: 2oef 2oeg
17452341 T.Ventriglia, M.A.Ballicora, P.Crevillén, J.Preiss, and J.M.Romero (2007).
Regulatory properties of potato-Arabidopsis hybrid ADP-glucose pyrophosphorylase.
  Plant Cell Physiol, 48, 875-880.  
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 code is shown on the right.