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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROTEIN KINASE DOMAIN OF YEAST AMP-ACTIVATED PROTEIN KINASE SNF1
 
Authors :  M. J. Rudolph, G. A. Amodeo, Y. Bai, L. Tong
Date :  22 Jun 09  (Deposition) - 30 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Kinase Domain, Transferase, Atp-Binding, Carbohydrate Metabolism, Kinase, Membrane, Nucleotide-Binding, Nucleus, Phosphoprotein, Serine/Threonine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Rudolph, G. A. Amodeo, Y. Bai, L. Tong
Crystal Structure Of The Protein Kinase Domain Of Yeast Amp-Activated Protein Kinase Snf1
Biochem. Biophys. Res. Commun. V. 337 1224 2005
PubMed-ID: 16236260  |  Reference-DOI: 10.1016/J.BBRC.2005.09.181

(-) Compounds

Molecule 1 - CARBON CATABOLITE-DEREPRESSING PROTEIN KINASE
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN
    GeneCAT1, CCR1, D8035.20, GLC2, PAS14, SNF1, YDR477W
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

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

(-) Sites  (0, 0)

(no "Site" information available for 3HYH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_YEAST61-84
 
  2A:61-84
B:61-84
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_YEAST173-185
 
  2A:173-185
B:173-185
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_YEAST61-84
 
  1A:61-84
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_YEAST173-185
 
  1A:173-185
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_YEAST61-84
 
  1-
B:61-84
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_YEAST173-185
 
  1-
B:173-185
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SNF1_YEAST61-84
 
  2A:61-84
B:61-84
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SNF1_YEAST173-185
 
  2A:173-185
B:173-185

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR477W1YDR477W.1IV:1412366-14142671902SNF1_YEAST1-6336332A:54-315 (gaps)
B:54-315 (gaps)
262
262

(-) 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:238
 aligned with SNF1_YEAST | P06782 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:262
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
           SNF1_YEAST    54 NYQIVKTLGEGSFGKVKLAYHTTTGQKVALKIINKKVLAKSDMQGRIEREISYLRLLRHPHIIKLYDVIKSKDEIIMVIEYAGNELFDYIVQRDKMSEQEARRFFQQIISAVEYCHRHKIVHRDLKPENLLLDEHLNVKIADFGLSNIMTDGNFLKTSCGSPNYAAPEVISGKLYAGPEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVYTLPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVDLPEYLL 315
               SCOP domains d3hyha_ A:    automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.---..eeeee......eeeeeeee..------hhhhhhhhhhhhhhh.......eeeeee...eeeeeee...eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee......---------------....hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:54-315 (gaps) UniProt: 1-633 [INCOMPLETE]                                                                                                                                                                                                             Transcript 1
                 3hyh A  54 NYQIVKTLGE---GKVKLAYHTTTGQKVALKIINKK------MQGRIEREISYLRLLRHPHIIKLYDVIKSKDEIIMVIEYAGNELFDYIVQRDKMSEQEARRFFQQIISAVEYCHRHKIVHRDLKPENLLLDEHLNVKIADFGLS---------------PNYAAPEVISGKLYAGPEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVYTLPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVDLPEYLL 315
                                    63   |    73        83     |   -  |    103       113       123       133       143       153       163       173       183       193     |   -         - |     223       233       243       253       263       273       283       293       303       313  
                                    63  67                    89     96                                                                                                    199             215                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with SNF1_YEAST | P06782 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:262
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
           SNF1_YEAST    54 NYQIVKTLGEGSFGKVKLAYHTTTGQKVALKIINKKVLAKSDMQGRIEREISYLRLLRHPHIIKLYDVIKSKDEIIMVIEYAGNELFDYIVQRDKMSEQEARRFFQQIISAVEYCHRHKIVHRDLKPENLLLDEHLNVKIADFGLSNIMTDGNFLKTSCGSPNYAAPEVISGKLYAGPEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVYTLPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVDLPEYLL 315
               SCOP domains d3hyhb_ B:     automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........----.eeeee......eeeeeee....-----hhhhhhhhhhhhhhh.......eeeeee....eeeeee...eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......---------------....hhhhhh-----.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:54-315 (gaps) UniProt: 1-633 [INCOMPLETE]                                                                                                                                                                                                             Transcript 1
                 3hyh B  54 NYQIVKTLGE----KVKLAYHTTTGQKVALKIINKKV-----MQGRIEREISYLRLLRHPHIIKLYDVIKSKDEIIMVIEYAGNELFDYIVQRDKMSEQEARRFFQQIISAVEYCHRHKIVHRDLKPENLLLDEHLNVKIADFGLS---------------PNYAAPEVIS-----GPEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVYTLPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVDLPEYLL 315
                                    63    |   73        83      |  -  |    103       113       123       133       143       153       163       173       183       193     |   -         - |     223|     |233       243       253       263       273       283       293       303       313  
                                    63   68                    90    96                                                                                                    199             215      224   230                                                                                     

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 3FAM: 2,4)

(no "CATH Domain" information available for 3HYH, only for superseded entry 3FAM replaced by 3HYH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SNF1_YEAST | P06782)
molecular function
    GO:0004679    AMP-activated protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of AMP.
    GO:0005086    ARF guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    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: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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0006995    cellular response to nitrogen starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.
    GO:0071940    fungal-type cell wall assembly    The aggregation, arrangement and bonding together of a set of components to form a fungal-type cell wall.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0001403    invasive growth in response to glucose limitation    A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1900436    positive regulation of filamentous growth of a population of unicellular organisms in response to starvation    Any process that activates or increases the frequency, rate or extent of filamentous growth of a population of unicellular organisms in response to starvation.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    GO:0016239    positive regulation of macroautophagy    Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007124    pseudohyphal growth    A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate.
    GO:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
    GO:0006986    response to unfolded protein    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0090606    single-species surface biofilm formation    A process in which planktonically growing microorganisms of the same species grow at the surface of a liquid-air interface and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000324    fungal-type vacuole    A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005641    nuclear envelope lumen    The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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_YEAST | P067822fh9 2qlv 3dae 3mn3 3t4n 3tdh 3te5

(-) Related Entries Specified in the PDB File

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