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PDBsum entry 2ya3
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protein ligands Protein-protein interface(s) links
Transferase PDB id
2ya3

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
102 a.a.
68 a.a.
300 a.a.
Ligands
J7V ×2
AMP
Waters ×142
PDB id:
2ya3
Name: Transferase
Title: Structure of the regulatory fragment of mammalian ampk in complex with coumarin adp
Structure: 5'-amp-activated protein kinase catalytic subunit alpha-1. Chain: a. Fragment: residues 407-555. Synonym: ampk subunit alpha-1. Engineered: yes. Other_details: the residues from a 393-395 and 545-550 are artificial as a result of cloning strategy. 5'-amp-activated protein kinase subunit beta-2. Chain: b.
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562
Resolution:
2.51Å     R-factor:   0.225     R-free:   0.263
Authors: B.Xiao,M.J.Sanders,E.Underwood,R.Heath,F.Mayer,D.Carmena,C.Jing, P.A.Walker,J.F.Eccleston,L.F.Haire,P.Saiu,S.A.Howell,R.Aasland, S.R.Martin,D.Carling,S.J.Gamblin
Key ref: B.Xiao et al. (2011). Structure of mammalian AMPK and its regulation by ADP. Nature, 472, 230-233. PubMed id: 21399626
Date:
17-Feb-11     Release date:   16-Mar-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P54645  (AAPK1_RAT) -  5'-AMP-activated protein kinase catalytic subunit alpha-1 from Rattus norvegicus
Seq:
Struc: 		 
Seq:
Struc: 		559 a.a.
102 a.a.*
Protein chain
Pfam   ArchSchema ?
O43741  (AAKB2_HUMAN) -  5'-AMP-activated protein kinase subunit beta-2 from Homo sapiens
Seq:
Struc: 		272 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
P80385  (AAKG1_RAT) -  5'-AMP-activated protein kinase subunit gamma-1 from Rattus norvegicus
Seq:
Struc: 		330 a.a.
300 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chain A: 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]
Bound ligand (Het Group name = J7V)
matches with 56.52% similarity 		+ ADP
 + H(+)
L-threonyl-[protein]
 + ATP
 = O-phospho-L-threonyl-[protein]
Bound ligand (Het Group name = J7V)
matches with 56.52% similarity 		+ ADP
 + H(+)
   Enzyme class 2: Chain A: E.C.2.7.11.26  - [tau protein] kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. L-seryl-[tau protein] + ATP = O-phospho-L-seryl-[tau protein] + ADP + H+
2. L-threonyl-[tau protein] + ATP = O-phospho-L-threonyl-[tau protein] + ADP + H+
L-seryl-[tau protein]
 + ATP
 = O-phospho-L-seryl-[tau protein]
Bound ligand (Het Group name = J7V)
matches with 56.52% similarity 		+ ADP
 + H(+)
L-threonyl-[tau protein]
 + ATP
 = O-phospho-L-threonyl-[tau protein]
Bound ligand (Het Group name = J7V)
matches with 56.52% similarity 		+ ADP
 + H(+)
   Enzyme class 3: Chain A: E.C.2.7.11.31  - [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ATP = O-phospho-L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ADP + H+
L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase]
 + ATP
 = O-phospho-L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase]
Bound ligand (Het Group name = J7V)
matches with 56.52% similarity 		+ ADP
 + H(+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Nature 472:230-233 (2011)
PubMed id: 21399626  
 
 
Structure of mammalian AMPK and its regulation by ADP.
B.Xiao, M.J.Sanders, E.Underwood, R.Heath, F.V.Mayer, D.Carmena, C.Jing, P.A.Walker, J.F.Eccleston, L.F.Haire, P.Saiu, S.A.Howell, R.Aasland, S.R.Martin, D.Carling, S.J.Gamblin.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22436748 D.G.Hardie, F.A.Ross, and S.A.Hawley (2012).
AMPK: a nutrient and energy sensor that maintains energy homeostasis.
  Nat Rev Mol Cell Biol, 13, 251-262.  
22659875 L.Chen, J.Wang, Y.Y.Zhang, S.F.Yan, D.Neumann, U.Schlattner, Z.X.Wang, and J.W.Wu (2012).
AMP-activated protein kinase undergoes nucleotide-dependent conformational changes.
  Nat Struct Mol Biol, 19, 716-718.
PDB codes: 4eag 4eai 4eaj 4eak 4eal
22318606 Y.Y.Lin, S.Kiihl, Y.Suhail, S.Y.Liu, Y.H.Chou, Z.Kuang, J.Y.Lu, C.N.Khor, C.L.Lin, J.S.Bader, R.Irizarry, and J.D.Boeke (2012).
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.
  Nature, 482, 251-255.  
21490664 D.G.Hardie (2011).
Signal transduction: How cells sense energy.
  Nature, 472, 176-177.  
21892142 M.M.Mihaylova, and R.J.Shaw (2011).
The AMPK signalling pathway coordinates cell growth, autophagy and metabolism.
  Nat Cell Biol, 13, 1016-1023.  
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
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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