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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH AN ALLOSTERIC ACTIVATOR BOUND TO THE PIF-POCKET
 
Authors :  V. Hindie, P. M. Alzari, R. M. Biondi
Date :  09 Jun 09  (Deposition) - 15 Sep 09  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Agc Kinase, Phosphorylation, Allostery, Pdk1, Pif-Pocket, Alpha-C Helix, Activation Loop, Atp Binding, Atp-Binding, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Hindie, A. Stroba, H. Zhang, L. A. Lopez-Garcia, L. Idrissova, S. Zeuzem, D. Hirschberg, F. Schaeffer, T. J. Jrgensen, M. Engel, P. M. Alzari, R. M. Biondi
Structure And Allosteric Effects Of Low-Molecular-Weight Activators On The Protein Kinase Pdk1.
Nat. Chem. Biol. V. 5 758 2009
PubMed-ID: 19718043  |  Reference-DOI: 10.1038/NCHEMBIO.208
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1
    Cell LineSF9
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentPDK1 KINASE DOMAIN
    GenePDK1, PDPK1
    MutationYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHPDK1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3P471Ligand/Ion(2Z)-5-(4-CHLOROPHENYL)-3-PHENYLPENT-2-ENOIC ACID
4SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:16 , GLY A:89 , GLY A:91 , SER A:92 , SER A:94 , VAL A:96 , ALA A:109 , LYS A:111 , SER A:160 , ALA A:162 , GLU A:166 , LEU A:212 , ASP A:223 , HOH A:363 , HOH A:395 , HOH A:403 , HOH A:441 , HOH A:467 , HOH A:471 , HOH A:474 , HOH A:506BINDING SITE FOR RESIDUE ATP A 1373
2AC2SOFTWARELYS A:76 , ILE A:119 , VAL A:127 , ARG A:131 , THR A:148 , PHE A:149 , GLN A:150 , LEU A:155 , TYR A:156 , PHE A:157 , HOH A:393BINDING SITE FOR RESIDUE P47 A 1374
3AC3SOFTWAREPRO A:307 , LYS A:308 , ASP A:311 , HIS A:339 , PRO A:340 , HOH A:382BINDING SITE FOR RESIDUE EPE A 1375
4AC4SOFTWAREARG A:172 , GLY A:175 , LEU A:254 , GLY A:278 , PHE A:291 , ALA A:292BINDING SITE FOR RESIDUE EPE A 1376

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PDPK1_HUMAN88-111  1A:88-111
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PDPK1_HUMAN201-213  1A:201-213

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003420851aENSE00001944688chr16:2587965-2588137173PDPK1_HUMAN1-880--
1.6cENST000003420856cENSE00001640744chr16:2607704-2607964261PDPK1_HUMAN9-95871A:75-9521
1.7ENST000003420857ENSE00001620065chr16:2611481-261152343PDPK1_HUMAN96-110151A:96-11015
1.8bENST000003420858bENSE00001694535chr16:2611772-2611909138PDPK1_HUMAN110-156471A:110-15647
1.9bENST000003420859bENSE00001744256chr16:2615554-2615698145PDPK1_HUMAN156-204491A:156-20449
1.10aENST0000034208510aENSE00001705748chr16:2616357-261645498PDPK1_HUMAN204-237341A:204-23734
1.13ENST0000034208513ENSE00001704745chr16:2627426-262750176PDPK1_HUMAN237-262261A:237-26226
1.14ENST0000034208514ENSE00001686272chr16:2631296-263136469PDPK1_HUMAN262-285241A:262-28524
1.15bENST0000034208515bENSE00001743545chr16:2631608-263170497PDPK1_HUMAN285-317331A:285-31733
1.16aENST0000034208516aENSE00001314244chr16:2633413-2633586174PDPK1_HUMAN318-375581A:318-35942
1.17ENST0000034208517ENSE00000946017chr16:2636677-2636894218PDPK1_HUMAN376-448730--
1.18ENST0000034208518ENSE00000946018chr16:2645794-264585158PDPK1_HUMAN448-467200--
1.19ENST0000034208519ENSE00000946019chr16:2647124-2647276153PDPK1_HUMAN468-518510--
1.20bENST0000034208520bENSE00001505218chr16:2647652-26531895538PDPK1_HUMAN519-556380--

(-) Sequences/Alignments

Asymmetric/Biological 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:285
 aligned with PDPK1_HUMAN | O15530 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:285
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354     
          PDPK1_HUMAN    75 RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
               SCOP domains d3hrfa_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3hrfA01 A:75-165 Phosphorylase Kinase; domain 1                                            3hrfA02 A:166-357 Transferase(Phosphotransferase) domain 1                                                                                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeee.....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...............hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c            Exon 1.7       ---------------------------------------------------------------------------------------------Exon 1.10a  PDB: A:204-237        ------------------------Exon 1.14  PDB: A:262-28--------------------------------Exon 1.16a  PDB: A:318-359 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.8b  PDB: A:110-156 UniProt: 110-156     --------------------------------------------------------------------------------Exon 1.13  PDB: A:237-262 ----------------------Exon 1.15b  PDB: A:285-317       ------------------------------------------ Transcript 1 (2)
           Transcript 1 (3) ---------------------------------------------------------------------------------Exon 1.9b  PDB: A:156-204 UniProt: 156-204       ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3hrf A  75 RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      |244       254       264       274       284       294       304       314       324       334       344       354     
                                                                                                                                                                                                241-SEP                                                                                                                  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 56)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDPK1_HUMAN | O15530)
molecular function
    GO:0004676    3-phosphoinositide-dependent protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of a phosphatidylinositol-3-phosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    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:0016004    phospholipase activator activity    Increases the activity of a phospholipase, an enzyme that catalyzes of the hydrolysis of a glycerophospholipid.
    GO:0043274    phospholipase binding    Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0032148    activation of protein kinase B activity    Any process that initiates the activity of the inactive enzyme protein kinase B.
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0071364    cellular response to epidermal growth factor stimulus    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 an epidermal growth factor stimulus.
    GO:0032869    cellular response to insulin stimulus    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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0097191    extrinsic apoptotic signaling pathway    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0006972    hyperosmotic response    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 detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
    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:0010667    negative regulation of cardiac muscle cell apoptotic process    Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0034122    negative regulation of toll-like receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor signaling pathway.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0090004    positive regulation of establishment of protein localization to plasma membrane    Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:0010518    positive regulation of phospholipase activity    Any process that increases the frequency, rate or extent of phospholipase activity, the hydrolysis of a phospholipid.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043122    regulation of I-kappaB kinase/NF-kappaB signaling    Any process that modulates I-kappaB kinase/NF-kappaB signaling.
    GO:0010594    regulation of endothelial cell migration    Any process that modulates the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0043304    regulation of mast cell degranulation    Any process that modulates the frequency, rate, or extent of mast cell degranulation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0003323    type B pancreatic cell development    The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDPK1_HUMAN | O155301h1w 1oky 1okz 1uu3 1uu7 1uu8 1uu9 1uvr 1w1d 1w1g 1w1h 1z5m 2biy 2pe0 2pe1 2pe2 2r7b 2vki 2xch 2xck 3h9o 3hrc 3ion 3iop 3nax 3nay 3nun 3nus 3nuu 3nuy 3orx 3orz 3otu 3pwy 3qc4 3qcq 3qcs 3qcx 3qcy 3qd0 3qd3 3qd4 3rcj 3rwp 3rwq 3sc1 4a06 4a07 4aw0 4aw1 4ct1 4ct2 4rqk 4rqv 4rrv 4xx9 5ack 5hkm 5hng 5ho7 5ho8 5lvl 5lvm 5lvn 5lvo 5lvp 5mrd

(-) Related Entries Specified in the PDB File

3hrc