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(-) Description

Title :  CRYSTAL STRUCTURE OF POMBE AMPK KDAID FRAGMENT
 
Authors :  L. Chen, Z. -H. Jiao, L. -S. Zheng, Y. -Y. Zhang, S. -T. Xie, Z. -X. Wang, J.
Date :  20 Apr 09  (Deposition) - 02 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ampk, Kinase, Atp-Binding, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Chen, Z. -H. Jiao, L. -S. Zheng, Y. -Y. Zhang, S. -T. Xie, Z. -X. Wang, J. -W. Wu
Structural Insight Into The Autoinhibition Mechanism Of Amp-Activated Protein Kinase
Nature V. 459 1122 2009
PubMed-ID: 19474788  |  Reference-DOI: 10.1038/NATURE08075

(-) Compounds

Molecule 1 - SNF1-LIKE PROTEIN KINASE SSP2
    ChainsB, A
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 25-351
    GeneSSP2
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    StrainSPQ-01
    SynonymAMPK KDAID

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x) B
Biological Unit 2 (1x)A 
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3H4J)

(-) Sites  (0, 0)

(no "Site" information available for 3H4J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H4J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H4J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H4J)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_SCHPO40-63
 
  2A:40-63
B:40-63
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_SCHPO152-164
 
  2A:152-164
B:152-164
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.SNF1_SCHPO316-345
 
  2A:316-345
B:316-345
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_SCHPO40-63
 
  1-
B:40-63
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_SCHPO152-164
 
  1-
B:152-164
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.SNF1_SCHPO316-345
 
  1-
B:316-345
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_SCHPO40-63
 
  1A:40-63
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_SCHPO152-164
 
  1A:152-164
-
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.SNF1_SCHPO316-345
 
  1A:316-345
-
Biological Unit 3 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_SCHPO40-63
 
  2A:40-63
B:40-63
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_SCHPO152-164
 
  2A:152-164
B:152-164
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.SNF1_SCHPO316-345
 
  2A:316-345
B:316-345

(-) Exons   (0, 0)

(no "Exon" information available for 3H4J)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:316
 aligned with SNF1_SCHPO | O74536 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:329
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347         
           SNF1_SCHPO    28 KRHIGPYIIRETLGEGSFGKVKLATHYKTQQKVALKFISRQLLKKSDMHMRVEREISYLKLLRHPHIIKLYDVITTPTDIVMVIEYAGGELFDYIVEKKRMTEDEGRRFFQQIICAIEYCHRHKIVHRDLKPENLLLDDNLNVKIADFGLSNIMTDGNFLKTSCGSPNYAAPEVINGKLYAGPEVDVWSCGIVLYVMLVGRLPFDDEFIPNLFKKVNSCVYVMPDFLSPGAQSLIRRMIVADPMQRITIQEIRRDPWFNVNLPDYLRPMEEVQGSYADSRIVSKLGEAMGFSEDYIVEALRSDENNEVKEAYNLLHENQVIQEKSHLSK 356
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhhh...hhhhhhhhhhh........eee......eeeeee....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh......hhh.eee.....eee.........hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh....hhhhh-----------.......hhhhhhhhhhhh........hhhhhh.hhhhhh....................hhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh--... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------UBA  PDB: A:316-345           ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4j A  28 KRHIGPYIIRETLGEGSFGKVKLATHYKTQQKVALKFISRQLLKKSDMHMRVEREISYLKLLRHPHIIKLYDVITTPTDIVMVIEYAGGELFDYIVEKKRMTEDEGRRFFQQIICAIEYCHRHKIVHRDLKPENLLLDDNLNVKIADFGLSNIMTDGNFLKTSCGSPNYAAPEVINGKLYAGPEVDVWSCGIVLYVMLVGRLPFDDEFI-----------YVMPDFLSPGAQSLIRRMIVADPMQRITIQEIRRDPWFNVNLPDYLRPMEEVQGSYADSRIVSKLGEAMGFSEDYIVEALRSDENNEVKEAYNLLHENQVIQEK--LEH 354
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227        |-         -|      257       267       277       287       297       307       317       327       337       347   |  |  
                                                                                                                                                                                                                                          236         248                                                                                                    351  |  
                                                                                                                                                                                                                                                                                                                                                                352  

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with SNF1_SCHPO | O74536 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:330
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
           SNF1_SCHPO    27 SKRHIGPYIIRETLGEGSFGKVKLATHYKTQQKVALKFISRQLLKKSDMHMRVEREISYLKLLRHPHIIKLYDVITTPTDIVMVIEYAGGELFDYIVEKKRMTEDEGRRFFQQIICAIEYCHRHKIVHRDLKPENLLLDDNLNVKIADFGLSNIMTDGNFLKTSCGSPNYAAPEVINGKLYAGPEVDVWSCGIVLYVMLVGRLPFDDEFIPNLFKKVNSCVYVMPDFLSPGAQSLIRRMIVADPMQRITIQEIRRDPWFNVNLPDYLRPMEEVQGSYADSRIVSKLGEAMGFSEDYIVEALRSDENNEVKEAYNLLHENQVIQEKSHLSK 356
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh..hhhhhhhhhhhh.........eeeeee...eeeeee....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee.........................hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhh....hhhhh.hhhhhh.hhhhhh..hhhhh..........hhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------UBA  PDB: B:316-345           ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h4j B  27 SKRHIGPYIIRETLGEGSFGKVKLATHYKTQQKVALKFISRQLLKKSDMHMRVEREISYLKLLRHPHIIKLYDVITTPTDIVMVIEYAGGELFDYIVEKKRMTEDEGRRFFQQIICAIEYCHRHKIVHRDLKPENLLLDDNLNVKIADFGLSNIMTDGNFLKTSCGSPNYAAPEVINGKLYAGPEVDVWSCGIVLYVMLVGRLPFDDEFIPNLFKKVNSCVYVMPDFLSPGAQSLIRRMIVADPMQRITIQEIRRDPWFNVNLPDYLRPMEEVQGSYADSRIVSKLGEAMGFSEDYIVEALRSDENNEVKEAYNLLHENQVIQEKLEHHH 356
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3H4J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H4J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H4J)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SNF1_SCHPO | O74536)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:1904262    negative regulation of TORC1 signaling    Any process that stops, prevents or reduces the frequency, rate or extent of TORC1 signaling.
    GO:2000766    negative regulation of cytoplasmic translation    Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0046015    regulation of transcription by glucose    Any process involving glucose that modulates the frequency, rate or extent or transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0044732    mitotic spindle pole body    The microtubule organizing center that forms as part of the mitotic cell cycle; functionally homologous to the animal cell centrosome.
    GO:0031588    nucleotide-activated protein kinase complex    A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SNF1_SCHPO | O745362oox 2ooy 2qr1 2qrc 2qrd 2qre

(-) Related Entries Specified in the PDB File

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