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PDBsum entry 1z0m

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protein ligands Protein-protein interface(s) links
Sugar binding protein PDB id
1z0m
Jmol
Contents
Protein chains
87 a.a. *
81 a.a. *
Ligands
BCD ×3
Waters ×200
* Residue conservation analysis
PDB id:
1z0m
Name: Sugar binding protein
Title: The glycogen-binding domain of the amp-activated protein kinase beta1 subunit
Structure: 5'-amp-activated protein kinase, beta-1 subunit. Chain: a, b, c. Fragment: 68-163 of beta1 subunit. Synonym: ampk beta-1 chain, ampkb, 40 kda subunit. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Not given
Resolution:
1.91Å     R-factor:   0.227     R-free:   0.243
Authors: G.Polekhina,A.Gupta,B.J.Van Denderen,S.C.Feil,B.E.Kemp, D.Stapleton,M.W.Parker
Key ref:
G.Polekhina et al. (2005). Structural basis for glycogen recognition by AMP-activated protein kinase. Structure, 13, 1453-1462. PubMed id: 16216577 DOI: 10.1016/j.str.2005.07.008
Date:
02-Mar-05     Release date:   25-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80386  (AAKB1_RAT) -  5'-AMP-activated protein kinase subunit beta-1
Seq:
Struc:
270 a.a.
87 a.a.
Protein chains
Pfam   ArchSchema ?
P80386  (AAKB1_RAT) -  5'-AMP-activated protein kinase subunit beta-1
Seq:
Struc:
270 a.a.
81 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.str.2005.07.008 Structure 13:1453-1462 (2005)
PubMed id: 16216577  
 
 
Structural basis for glycogen recognition by AMP-activated protein kinase.
G.Polekhina, A.Gupta, B.J.van Denderen, S.C.Feil, B.E.Kemp, D.Stapleton, M.W.Parker.
 
  ABSTRACT  
 
AMP-activated protein kinase (AMPK) coordinates cellular metabolism in response to energy demand as well as to a variety of stimuli. The AMPK beta subunit acts as a scaffold for the alpha catalytic and gamma regulatory subunits and targets the AMPK heterotrimer to glycogen. We have determined the structure of the AMPK beta glycogen binding domain in complex with beta-cyclodextrin. The structure reveals a carbohydrate binding pocket that consolidates all known aspects of carbohydrate binding observed in starch binding domains into one site, with extensive contact between several residues and five glucose units. beta-cyclodextrin is held in a pincer-like grasp with two tryptophan residues cradling two beta-cyclodextrin glucose units and a leucine residue piercing the beta-cyclodextrin ring. Mutation of key beta-cyclodextrin binding residues either partially or completely prevents the glycogen binding domain from binding glycogen. Modeling suggests that this binding pocket enables AMPK to interact with glycogen anywhere across the carbohydrate's helical surface.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Carbohydrate Binding to b-GBD
(A) Close up stereoview of the interactions between b-cyclodextrin and b-GBD.
(B) Stereoview of the maltoheptaose-b-GBD complex model. Both figures were produced with BOBSCRIPT and Raster3D (Merritt and Murphy, 1994).
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1453-1462) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265739 D.G.Hardie (2011).
AMP-activated protein kinase: a cellular energy sensor with a key role in metabolic disorders and in cancer.
  Biochem Soc Trans, 39, 1.  
21031502 C.Moffat, and M.Ellen Harper (2010).
Metabolic functions of AMPK: aspects of structure and of natural mutations in the regulatory gamma subunits.
  IUBMB Life, 62, 739-745.  
20679247 C.W.Vander Kooi, A.O.Taylor, R.M.Pace, D.A.Meekins, H.F.Guo, Y.Kim, and M.S.Gentry (2010).
Structural basis for the glucan phosphatase activity of Starch Excess4.
  Proc Natl Acad Sci U S A, 107, 15379-15384.
PDB code: 3nme
20391537 D.Stapleton, C.Nelson, K.Parsawar, D.McClain, R.Gilbert-Wilson, E.Barker, B.Rudd, K.Brown, W.Hendrix, P.O'Donnell, and G.Parker (2010).
Analysis of hepatic glycogen-associated proteins.
  Proteomics, 10, 2320-2329.  
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae.
  Mol Microbiol, 77, 183-199.
PDB codes: 2xd2 2xd3
20010958 J.Li, and L.D.McCullough (2010).
Effects of AMP-activated protein kinase in cerebral ischemia.
  J Cereb Blood Flow Metab, 30, 480-492.  
20702566 P.R.Matthews, M.Schindler, P.Howles, T.Arioli, and R.E.Williamson (2010).
A CESA from Griffithsia monilis (Rhodophyta, Florideophyceae) has a family 48 carbohydrate-binding module.
  J Exp Bot, 61, 4461-4468.  
19897735 S.Mangat, D.Chandrashekarappa, R.R.McCartney, K.Elbing, and M.C.Schmidt (2010).
Differential roles of the glycogen-binding domains of beta subunits in regulation of the Snf1 kinase complex.
  Eukaryot Cell, 9, 173-183.  
19245651 A.McBride, and D.G.Hardie (2009).
AMP-activated protein kinase--a sensor of glycogen as well as AMP and ATP?
  Acta Physiol (Oxf), 196, 99.  
19117544 A.McBride, S.Ghilagaber, A.Nikolaev, and D.G.Hardie (2009).
The glycogen-binding domain on the AMPK beta subunit allows the kinase to act as a glycogen sensor.
  Cell Metab, 9, 23-34.  
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
19196246 E.A.Richter, and N.B.Ruderman (2009).
AMPK and the biochemistry of exercise: implications for human health and disease.
  Biochem J, 418, 261-275.  
19422833 E.Ficko-Blean, and A.B.Boraston (2009).
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
  J Mol Biol, 390, 208-220.
PDB codes: 2w1q 2w1s 2w1u 2wdb
19382205 J.P.Turkenburg, A.M.Brzozowski, A.Svendsen, T.V.Borchert, G.J.Davies, and K.S.Wilson (2009).
Structure of a pullulanase from Bacillus acidopullulyticus.
  Proteins, 76, 516-519.
PDB code: 2wan
19245650 J.S.Oakhill, J.W.Scott, and B.E.Kemp (2009).
Structure and function of AMP-activated protein kinase.
  Acta Physiol (Oxf), 196, 3.  
  19956450 J.Wang, and J.Li (2009).
Activated protein C: a potential cardioprotective factor against ischemic injury during ischemia/reperfusion.
  Am J Transl Res, 1, 381-392.  
19448707 K.Baar (2009).
The signaling underlying FITness.
  Appl Physiol Nutr Metab, 34, 411-419.  
19139240 M.Palomo, S.Kralj, M.J.van der Maarel, and L.Dijkhuizen (2009).
The unique branching patterns of Deinococcus glycogen branching enzymes are determined by their N-terminal domains.
  Appl Environ Microbiol, 75, 1355-1362.  
19754155 S.Hsu, Y.Kim, S.Li, E.S.Durrant, R.M.Pace, V.L.Woods, and M.S.Gentry (2009).
Structural insights into glucan phosphatase dynamics using amide hydrogen-deuterium exchange mass spectrometry.
  Biochemistry, 48, 9891-9902.  
18698919 D.Konkolewicz, O.Thorn-Seshold, and A.Gray-Weale (2008).
Models for randomly hyperbranched polymers: Theory and simulation.
  J Chem Phys, 129, 054901.  
19022182 J.W.Scott, B.J.van Denderen, S.B.Jorgensen, J.E.Honeyman, G.R.Steinberg, J.S.Oakhill, T.J.Iseli, A.Koay, P.R.Gooley, D.Stapleton, and B.E.Kemp (2008).
Thienopyridone drugs are selective activators of AMP-activated protein kinase beta1-containing complexes.
  Chem Biol, 15, 1220-1230.  
18474591 M.Momcilovic, S.H.Iram, Y.Liu, and M.Carlson (2008).
Roles of the glycogen-binding domain and Snf4 in glucose inhibition of SNF1 protein kinase.
  J Biol Chem, 283, 19521-19529.  
17712357 D.G.Hardie (2007).
AMP-activated/SNF1 protein kinases: conserved guardians of cellular energy.
  Nat Rev Mol Cell Biol, 8, 774-785.  
16879084 D.G.Hardie (2007).
AMP-activated protein kinase as a drug target.
  Annu Rev Pharmacol Toxicol, 47, 185-210.  
17851534 G.A.Amodeo, M.J.Rudolph, and L.Tong (2007).
Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homologue SNF1.
  Nature, 449, 492-495.
PDB code: 2qlv
17652778 J.E.Brenman, and B.R.Temple (2007).
Opinion: alternative views of AMP-activated protein kinase.
  Cell Biochem Biophys, 47, 321-331.  
17728241 M.J.Sanders, Z.S.Ali, B.D.Hegarty, R.Heath, M.A.Snowden, and D.Carling (2007).
Defining the mechanism of activation of AMP-activated protein kinase by the small molecule A-769662, a member of the thienopyridone family.
  J Biol Chem, 282, 32539-32548.  
17646401 M.S.Gentry, R.H.Dowen, C.A.Worby, S.Mattoo, J.R.Ecker, and J.E.Dixon (2007).
The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease.
  J Cell Biol, 178, 477-488.  
17855357 O.Göransson, A.McBride, S.A.Hawley, F.A.Ross, N.Shpiro, M.Foretz, B.Viollet, D.G.Hardie, and K.Sakamoto (2007).
Mechanism of action of A-769662, a valuable tool for activation of AMP-activated protein kinase.
  J Biol Chem, 282, 32549-32560.  
17452784 P.Day, A.Sharff, L.Parra, A.Cleasby, M.Williams, S.Hörer, H.Nar, N.Redemann, I.Tickle, and J.Yon (2007).
Structure of a CBS-domain pair from the regulatory gamma1 subunit of human AMPK in complex with AMP and ZMP.
  Acta Crystallogr D Biol Crystallogr, 63, 587-596.
PDB codes: 2uv4 2uv5 2uv6 2uv7
17289942 R.Townley, and L.Shapiro (2007).
Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.
  Science, 315, 1726-1729.
PDB codes: 2oox 2ooy
17403675 R.Viana, M.C.Towler, D.A.Pan, D.Carling, B.Viollet, D.G.Hardie, and P.Sanz (2007).
A conserved sequence immediately N-terminal to the Bateman domains in AMP-activated protein kinase gamma subunits is required for the interaction with the beta subunits.
  J Biol Chem, 282, 16117-16125.  
17937917 X.Jin, R.Townley, and L.Shapiro (2007).
Structural insight into AMPK regulation: ADP comes into play.
  Structure, 15, 1285-1295.
PDB codes: 2qr1 2qrc 2qrd 2qre
17631110 X.Zhu, J.Sun, and Y.Hu (2007).
Determination of protein by hydroxypropyl-beta-cyclodextrin sensitized fluorescence quenching method with erythrosine sodium as a fluorescence probe.
  Anal Chim Acta, 596, 298-302.  
16644800 D.G.Hardie, S.A.Hawley, and J.W.Scott (2006).
AMP-activated protein kinase--development of the energy sensor concept.
  J Physiol, 574, 7.  
16623901 D.Kerk, T.R.Conley, F.A.Rodriguez, H.T.Tran, M.Nimick, D.G.Muench, and G.B.Moorhead (2006).
A chloroplast-localized dual-specificity protein phosphatase in Arabidopsis contains a phylogenetically dispersed and ancient carbohydrate-binding domain, which binds the polysaccharide starch.
  Plant J, 46, 400-413.  
16998529 G.R.Steinberg, S.L.Macaulay, M.A.Febbraio, and B.E.Kemp (2006).
AMP-activated protein kinase--the fat controller of the energy railroad.
  Can J Physiol Pharmacol, 84, 655-665.  
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.