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(-) Description

Title :  SOLUTION STRUCTURE OF THE C1 DOMAIN OF THE HUMAN DIACYLGLYCEROL KINASE DELTA
 
Authors :  K. Miyamoto, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 Oct 03  (Deposition) - 21 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  C1 Domain, Cystein-Rich Zinc Binding Domain, Diacylglycerol Kinase Delta, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Miyamoto, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The C1 Domain Of The Human Diacylglycerol Kinase Delta
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE, DELTA
    ChainsA
    EC Number2.7.1.107
    EngineeredYES
    Expression System PlasmidP030128-49
    Expression System Vector TypePLASMID
    FragmentC1 DOMAIN
    GeneKAZUSA CDNA HA00914
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymDIGLYCERIDE KINASE, DGK-DELTA, DAG KINASE DELTA, 130 KDA DIACYLGLYCEROL KINASE, DIACYLGLYCEROL KINASE DELTA(KIAA0145)

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:28 , CYS A:59 , CYS A:62 , CYS A:78BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:41 , CYS A:44 , HIS A:67 , CYS A:70BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R79)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R79)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R79)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_DAG_PE_2PS50081 Zinc finger phorbol-ester/DAG-type profile.DGKD_HUMAN163-213
235-286
  1-
A:27-78
2ZF_DAG_PE_1PS00479 Zinc finger phorbol-ester/DAG-type signature.DGKD_HUMAN164-213
236-286
  1-
A:28-78
3DAGKPS50146 DAG-kinase catalytic (DAGKc) domain profile.DGKD_HUMAN317-451  1A:79-84

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002640571aENSE00001123844chr2:234263153-234263320168DGKD_HUMAN1-52520--
1.4bENST000002640574bENSE00001656899chr2:234296903-234297013111DGKD_HUMAN53-89370--
1.5ENST000002640575ENSE00001663062chr2:234299049-23429912981DGKD_HUMAN90-116270--
1.8aENST000002640578aENSE00000403200chr2:234343026-234343130105DGKD_HUMAN117-151350--
1.9bENST000002640579bENSE00000786932chr2:234343415-234343547133DGKD_HUMAN152-196450--
1.10bENST0000026405710bENSE00000786931chr2:234344464-234344570107DGKD_HUMAN196-231361A:1-2323
1.11ENST0000026405711ENSE00000786930chr2:234344962-234345087126DGKD_HUMAN232-273421A:24-6542
1.12ENST0000026405712ENSE00000403204chr2:234346023-234346125103DGKD_HUMAN274-308351A:66-7813
1.13aENST0000026405713aENSE00000786928chr2:234346863-234347025163DGKD_HUMAN308-362551A:79-846
1.14aENST0000026405714aENSE00000786927chr2:234350533-234350641109DGKD_HUMAN362-398370--
1.15ENST0000026405715ENSE00000403207chr2:234354269-234354408140DGKD_HUMAN399-445470--
1.16ENST0000026405716ENSE00000786925chr2:234355358-23435544285DGKD_HUMAN445-473290--
1.18bENST0000026405718bENSE00000403209chr2:234356733-23435682795DGKD_HUMAN474-505320--
1.19ENST0000026405719ENSE00000403210chr2:234356922-234357021100DGKD_HUMAN505-538340--
1.20cENST0000026405720cENSE00000403211chr2:234357749-234358022274DGKD_HUMAN539-630920--
1.21ENST0000026405721ENSE00000403212chr2:234358628-234358777150DGKD_HUMAN630-680510--
1.22ENST0000026405722ENSE00000786920chr2:234359568-234359696129DGKD_HUMAN680-723440--
1.23ENST0000026405723ENSE00000403214chr2:234360610-23436070697DGKD_HUMAN723-755330--
1.25ENST0000026405725ENSE00002197667chr2:234363409-234363519111DGKD_HUMAN755-792380--
1.26ENST0000026405726ENSE00001711050chr2:234365545-23436564197DGKD_HUMAN792-824330--
1.27aENST0000026405727aENSE00001780674chr2:234365867-234365974108DGKD_HUMAN825-860360--
1.28bENST0000026405728bENSE00001677254chr2:234366930-234367043114DGKD_HUMAN861-898380--
1.29bENST0000026405729bENSE00001758296chr2:234368403-234368537135DGKD_HUMAN899-943450--
1.30ENST0000026405730ENSE00001604181chr2:234368840-234368991152DGKD_HUMAN944-994510--
1.31ENST0000026405731ENSE00001593353chr2:234370994-234371105112DGKD_HUMAN994-1031380--
1.32ENST0000026405732ENSE00001681592chr2:234371289-23437138193DGKD_HUMAN1032-1062310--
1.33bENST0000026405733bENSE00001695731chr2:234372810-234372929120DGKD_HUMAN1063-1102400--
1.34bENST0000026405734bENSE00001756067chr2:234375732-234375849118DGKD_HUMAN1103-1142400--
1.35ENST0000026405735ENSE00001737904chr2:234377069-234377199131DGKD_HUMAN1142-1185440--
1.36bENST0000026405736bENSE00001923484chr2:234378017-2343807462730DGKD_HUMAN1186-1214290--

(-) Sequences/Alignments

NMR Structure
   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:84
 aligned with DGKD_HUMAN | Q16760 from UniProtKB/Swiss-Prot  Length:1214

    Alignment length:127
                                   218       228       238       248       258       268       278       288       298       308       318       328       
           DGKD_HUMAN   209 ATNNCKWTTLASIGKDIIEDADGIAMPHQWLEGNLPVSAKCTVCDKTCGSVLRLQDWRCLWCKAMVHTSCKESLLTKCPLGLCKVSVIPPTALNSIDSDGFWKASCPPSCTSPLLVFVNSKSGDNQG 335
               SCOP domains d1r79a_ A: Diacylglycerol kinase delta                                                                                          SCOP domains
               CATH domains ------------------------1r79A01 A:25-79  [code=3.30.60.20, no name defined]                                               ----- CATH domains
               Pfam domains ---------------------------C1_1-1r79A01 A:28-78                               ------------------------------------------------- Pfam domains
         Sec.struct. author .............................eee........................eee.....ee.hhhhhh.....-------------------------------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ZF_DA---------------------ZF_DAG_PE_2  PDB: A:27-78 UniProt: 235-286          ------------------------------DAGK  PDB: A:79-84  PROSITE (1)
                PROSITE (2) ZF_DA----------------------ZF_DAG_PE_1  PDB: A:28-78 UniProt: 236-286         ------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10b  PDB: A:1-23Exon 1.11  PDB: A:24-65 UniProt: 232-273  Exon 1.12  PDB: A:66-78            --------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------Exon 1.13a  PDB: A:79-84     Transcript 1 (2)
                 1r79 A   1 GSSGSSGTTLASIGKDIIEDADGIAMPHQWLEGNLPVSAKCTVCDKTCGSVLRLQDWRCLWCKAMVHTSCKESLLTKC-------------------------------------------SGPSSG  84
                                    10        20        30        40        50        60        70       | -         -         -         -         - |     
                                                                                                        78                                          79     

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: C1 (13)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (DGKD_HUMAN | Q16760)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019992    diacylglycerol binding    Interacting selectively and non-covalently with diacylglycerol, a diester of glycerol and two fatty acids.
    GO:0004143    diacylglycerol kinase activity    Catalysis of the reaction: NTP + 1,2-diacylglycerol = NDP + 1,2-diacylglycerol-3-phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0046339    diacylglycerol metabolic process    The chemical reactions and pathways involving diacylglycerol, a glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    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: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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0007205    protein kinase C-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of protein kinase C (PKC). PKC is activated by second messengers including diacylglycerol (DAG).
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010033    response to organic substance    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 organic substance stimulus.
    GO:0019932    second-messenger-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via a second messenger; a small molecule or ion that can be quickly generated or released from intracellular stores, and can diffuse within the cell. Second-messenger signaling includes production or release of the second messenger, and effectors downstream of the second messenger that further transmit the signal within the cell.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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

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        DGKD_HUMAN | Q167603bq7

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