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(-) Description

Title :  YAP65 WW DOMAIN COMPLEXED TO N-(N-OCTYL)-GPPPY-NH2
 
Authors :  J. R. Pires, F. Taha-Nejad, F. Toepert, T. Ast, U. Hoffmuller, J. Schneider-Mergener, R. Kuhne, M. J. Macias, H. Oschkinat
Date :  30 Oct 01  (Deposition) - 28 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Ww Domain, Yap65, Beta-Sheet Proteins, Ligands, Proline- Rich Peptides, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Pires, F. Taha-Nejad, F. Toepert, T. Ast, U. Hoffmuller, J. Schneider-Mergener, R. Kuhne, M. J. Macias, H. Oschkinat
Solution Structures Of The Yap65 Ww Domain And The Variant L30 K In Complex With The Peptides Gtppppytvg, N-(N-Octyl)-Gpppy And Plppy And The Application Of Peptide Libraries Reveal A Minimal Binding Epitope.
J. Mol. Biol. V. 314 1147 2001
PubMed-ID: 11743730  |  Reference-DOI: 10.1006/JMBI.2000.5199
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 65 KDA YES-ASSOCIATED PROTEIN
    Chains: A
    Engineered: YES
    Fragment: WILD TYPE WW DOMAIN
    Other Details: THIS SEQUENCE WAS SYNTHETICALLY OBTAINED, BY SEMIAUTOMATED SPOT SYNTHESIS IN A CELLULOSE SUPPORT.
    Synonym: YAP65
    Synthetic: YES
 
Molecule 2 - WW DOMAIN BINDING PROTEIN-1
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 149-153
    Mutation: YES
    Other Details: THIS SEQUENCE WAS SYNTHETICALLY OBTAINED BY SPOT SYNTHESIS IN A CELLULOSE SUPPORT.
    Synonym: WBP-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2OCT1Ligand/IonN-OCTANE
NMR Structure * (2, 2)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2OCT1Ligand/IonN-OCTANE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:3BINDING SITE FOR RESIDUE OCT B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K9Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K9Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K9Q)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_2PS50020 WW/rsp5/WWP domain profile.YAP1_HUMAN171-204
230-263		  1A:11-44
-
2WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.YAP1_HUMAN177-202
236-261		  1A:17-42
-
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_2PS50020 WW/rsp5/WWP domain profile.YAP1_HUMAN171-204
230-263		  1A:11-44
-
2WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.YAP1_HUMAN177-202
236-261		  1A:17-42
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002824411aENSE00002151482chr11:101981192-101981900709YAP1_HUMAN1-1071070--
1.3ENST000002824413ENSE00001105700chr11:101984875-101985125251YAP1_HUMAN108-191841A:5-3127
1.4ENST000002824414ENSE00001105694chr11:102033187-102033302116YAP1_HUMAN191-230401A:31-4414
1.5aENST000002824415aENSE00001311988chr11:102056749-102056862114YAP1_HUMAN230-268390--
1.6aENST000002824416aENSE00001292600chr11:102076624-102076805182YAP1_HUMAN268-328610--
1.7ENST000002824417ENSE00001321313chr11:102080248-10208029548YAP1_HUMAN329-344160--
1.8ENST000002824418ENSE00001105702chr11:102094353-102094483131YAP1_HUMAN345-388440--
1.10ENST0000028244110ENSE00001105705chr11:102098200-102098312113YAP1_HUMAN388-426390--
1.11fENST0000028244111fENSE00001345991chr11:102100433-1021041543722YAP1_HUMAN426-504790--

(-) 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:40
 aligned with YAP1_HUMAN | P46937 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:40
                                   174       184       194       204
           YAP1_HUMAN   165 FEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRK 204
               SCOP domains d1k9qa_ A: Yap65 ww domain               SCOP domains
               CATH domains 1k9qA00 A:5-44                           CATH domains
               Pfam domains --------WW-1k9qA01 A:13-42            -- Pfam domains
         Sec.struct. author ............eeeee.....eeeee....eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                PROSITE (1) ------WW_DOMAIN_2  PDB: A:11-44          PROSITE (1)
                PROSITE (2) ------------WW_DOMAIN_1  PDB: A:17-42 -- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:5-31      ------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.4       Transcript 1 (2)
                 1k9q A   5 FEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRK  44
                                    14        24        34        44


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1k9q B   3 GPPPYx   8
                                 |
                                 8-NH2
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: WW] (77)

(-) Gene Ontology  (49, 49)

NMR Structure(hide GO term definitions)
Chain A   (YAP1_HUMAN | P46937)
molecular function
    GO:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0001076    transcription factor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0060449    bud elongation involved in lung branching    The process in which a bud in the lung grows out from the point where it is formed.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    cellular response to DNA damage 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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071480    cellular response to gamma radiation    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 a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0071300    cellular response to retinoic acid    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 a retinoic acid stimulus.
    GO:0060242    contact inhibition    The cellular process in which cells stop growing or dividing in response to increased cell density.
    GO:0003143    embryonic heart tube morphogenesis    The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
    GO:0035329    hippo signaling    The series of molecular signals mediated by the serine/threonine kinase Hippo or one of its orthologs. In Drosophila, Hippo in complex with the scaffold protein Salvador (Sav), phosphorylates and activates Warts (Wts), which in turn phosphorylates and inactivates the Yorkie (Yki) transcriptional activator. The core fly components hippo, sav, wts and mats are conserved in mammals as STK4/3 (MST1/2), SAV1/WW45, LATS1/2 and MOB1.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0048368    lateral mesoderm development    The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure.
    GO:0060487    lung epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung.
    GO:0030857    negative regulation of epithelial cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation.
    GO:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:2000737    negative regulation of stem cell differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation.
    GO:0030903    notochord development    The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
    GO:0048339    paraxial mesoderm development    The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0046622    positive regulation of organ growth    Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism.
    GO:1902459    positive regulation of stem cell population maintenance    Any process that activates or increases the frequency, rate or extent of stem cell population maintenance.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0060828    regulation of canonical Wnt signaling pathway    Any process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0010837    regulation of keratinocyte proliferation    Any process that modulates the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population.
    GO:0072307    regulation of metanephric nephron tubule epithelial cell differentiation    Any process that modulates the frequency, rate or extent of metanephric nephron tubule epithelial cell differentiation.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0072091    regulation of stem cell proliferation    Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
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: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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YAP1_HUMAN | P46937: 1jmq 1k5r 1k9r 2law 2lax 2lay 2ltv 2ltw 3kys 3mhr 4re1 4rex

(-) Related Entries Specified in the PDB File

1e0m 1E0M CONTAINS PROTOTYPE WW DOMAIN
1eg3 1EG3 CONTAINS DYSTROPHIN WW DOMAIN FRAGMENT
1eg4 1EG4 CONTAINS DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEXED WITH BETA-DYSTROGLYCAN PEPTIDE
1i5h 1I5H CONTAINS RNEDD4 WWIII DOMAIN-RENAC BP2 PEPTIDE COMPLEX
1jmq 1JMQ CONTAINS YAP65 (L30K MUTANT) WW DOMAIN IN COMPLEXED WITH GTPPPPYTVG PEPTIDE
1k9r 1K9R CONTAINS YAP65 WW DOMAIN COMPLEXED WITH ACETYL-PLPPY