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PDBsum entry 3hyh
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protein Protein-protein interface(s) links
Transferase PDB id
3hyh

 

 

 

 

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Contents
Protein chains
238 a.a. *
Waters ×107
* Residue conservation analysis
PDB id:
3hyh
Name: Transferase
Title: Crystal structure of the protein kinase domain of yeast amp-activated protein kinase snf1
Structure: Carbon catabolite-derepressing protein kinase. Chain: a, b. Fragment: kinase domain. Engineered: yes
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: cat1, ccr1, d8035.20, glc2, pas14, snf1, ydr477w. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.241     R-free:   0.280
Authors: M.J.Rudolph,G.A.Amodeo,Y.Bai,L.Tong
Key ref: M.J.Rudolph et al. (2005). Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1. Biochem Biophys Res Commun, 337, 1224-1228. PubMed id: 16236260 DOI: 10.1016/j.bbrc.2005.09.181
Date:
22-Jun-09     Release date:   30-Jun-09    
Supersedes: 3fam
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06782  (SNF1_YEAST) -  Carbon catabolite-derepressing protein kinase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		633 a.a.
238 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.1  - non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H+
2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H+
L-seryl-[protein]
 + ATP
 = O-phospho-L-seryl-[protein]
 + ADP
 + H(+)
L-threonyl-[protein]
 + ATP
 = O-phospho-L-threonyl-[protein]
 + ADP
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/j.bbrc.2005.09.181 Biochem Biophys Res Commun 337:1224-1228 (2005)
PubMed id: 16236260  
 
 
Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1.
M.J.Rudolph, G.A.Amodeo, Y.Bai, L.Tong.
 
  ABSTRACT  
 
AMP-activated protein kinase (AMPK) is a master metabolic regulator, and is an important target for drug development against diabetes, obesity, and other diseases. AMPK is a hetero-trimeric enzyme, with a catalytic (alpha) subunit, and two regulatory (beta and gamma) subunits. Here we report the crystal structure at 2.2A resolution of the protein kinase domain (KD) of the catalytic subunit of yeast AMPK (commonly known as SNF1). The Snf1-KD structure shares strong similarity to other protein kinases, with a small N-terminal lobe and a large C-terminal lobe. Two negative surface patches in the structure may be important for the recognition of the substrates of this kinase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481774 L.Zhu, L.Chen, X.M.Zhou, Y.Y.Zhang, Y.J.Zhang, J.Zhao, S.R.Ji, J.W.Wu, and Y.Wu (2011).
Structural Insights into the Architecture and Allostery of Full-Length AMP-Activated Protein Kinase.
  Structure, 19, 515-522.  
21543851 N.Handa, T.Takagi, S.Saijo, S.Kishishita, D.Takaya, M.Toyama, T.Terada, M.Shirouzu, A.Suzuki, S.Lee, T.Yamauchi, M.Okada-Iwabu, M.Iwabu, T.Kadowaki, Y.Minokoshi, and S.Yokoyama (2011).
Structural basis for compound C inhibition of the human AMP-activated protein kinase α2 subunit kinase domain.
  Acta Crystallogr D Biol Crystallogr, 67, 480-487.
PDB codes: 2yza 3aqv
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.  
  20823513 M.J.Rudolph, G.A.Amodeo, and L.Tong (2010).
An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 999.
PDB code: 3mn3
19492062 A.A.Santos, C.M.Carvalho, L.H.Florentino, H.J.Ramos, and E.P.Fontes (2009).
Conserved threonine residues within the A-loop of the receptor NIK differentially regulate the kinase function required for antiviral signaling.
  PLoS One, 4, e5781.  
19474788 L.Chen, Z.H.Jiao, L.S.Zheng, Y.Y.Zhang, S.T.Xie, Z.X.Wang, and J.W.Wu (2009).
Structural insight into the autoinhibition mechanism of AMP-activated protein kinase.
  Nature, 459, 1146-1149.
PDB codes: 3dae 3h4j
19651772 R.Scholz, M.Suter, T.Weimann, C.Polge, P.V.Konarev, R.F.Thali, R.D.Tuerk, B.Viollet, T.Wallimann, U.Schlattner, and D.Neumann (2009).
Homo-oligomerization and activation of AMP-activated protein kinase are mediated by the kinase domain alphaG-helix.
  J Biol Chem, 284, 27425-27437.  
17981722 K.Hedbacker, and M.Carlson (2008).
SNF1/AMPK pathways in yeast.
  Front Biosci, 13, 2408-2420.  
18079111 T.J.Iseli, J.S.Oakhill, M.F.Bailey, S.Wee, M.Walter, B.J.van Denderen, L.A.Castelli, F.Katsis, L.A.Witters, D.Stapleton, S.L.Macaulay, B.J.Michell, and B.E.Kemp (2008).
AMP-activated protein kinase subunit interactions: beta1:gamma1 association requires beta1 Thr-263 and Tyr-267.
  J Biol Chem, 283, 4799-4807.  
18314332 T.Williams, and J.E.Brenman (2008).
LKB1 and AMPK in cell polarity and division.
  Trends Cell Biol, 18, 193-198.  
18372250 U.Riek, R.Scholz, P.Konarev, A.Rufer, M.Suter, A.Nazabal, P.Ringler, M.Chami, S.A.Müller, D.Neumann, M.Forstner, M.Hennig, R.Zenobi, A.Engel, D.Svergun, U.Schlattner, and T.Wallimann (2008).
Structural properties of AMP-activated protein kinase: dimerization, molecular shape, and changes upon ligand binding.
  J Biol Chem, 283, 18331-18343.  
17937905 B.E.Kemp, J.S.Oakhill, and J.W.Scott (2007).
AMPK structure and regulation from three angles.
  Structure, 15, 1161-1163.  
17851531 B.Xiao, R.Heath, P.Saiu, F.C.Leiper, P.Leone, C.Jing, P.A.Walker, L.Haire, J.F.Eccleston, C.T.Davis, S.R.Martin, D.Carling, and S.J.Gamblin (2007).
Structural basis for AMP binding to mammalian AMP-activated protein kinase.
  Nature, 449, 496-500.
PDB codes: 2v8q 2v92 2v9j
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.  
17255938 J.W.Scott, F.A.Ross, J.K.Liu, and D.G.Hardie (2007).
Regulation of AMP-activated protein kinase by a pseudosubstrate sequence on the gamma subunit.
  EMBO J, 26, 806-815.  
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
17116308 R.A.Miller, B.F.Binkowski, and P.J.Belshaw (2007).
Ligand-regulated peptide aptamers that inhibit the 5'-AMP-activated protein kinase.
  J Mol Biol, 365, 945-957.  
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
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
16803889 A.Marx, C.Nugoor, J.Müller, S.Panneerselvam, T.Timm, M.Bilang, E.Mylonas, D.I.Svergun, E.M.Mandelkow, and E.Mandelkow (2006).
Structural variations in the catalytic and ubiquitin-associated domains of microtubule-associated protein/microtubule affinity regulating kinase (MARK) 1 and MARK2.
  J Biol Chem, 281, 27586-27599.
PDB code: 2hak
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.  
17079130 P.Pellicena, and J.Kuriyan (2006).
Protein-protein interactions in the allosteric regulation of protein kinases.
  Curr Opin Struct Biol, 16, 702-709.  
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.

 

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