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(-) Description

Title :  SOLUTION STRUCTURE OF BEM1P PB1 DOMAIN COMPLEXED WITH CDC24P PB1 DOMAIN
 
Authors :  Y. Kobashigawa, S. Yoshinaga, T. Tandai, K. Ogura, F. Inagaki
Date :  23 Feb 09  (Deposition) - 06 Oct 09  (Release) - 06 Oct 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Pb1, Budding, Yeast, Phox, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ogura, T. Tandai, S. Yoshinaga, Y. Kobashigawa, H. Kumeta, T. Ito, H. Sumimoto, F. Inagaki
Nmr Structure Of The Heterodimer Of Bem1 And Cdc24 Pb1 Domains From Saccharomyces Cerevisiae
J. Biochem. V. 146 317 2009
PubMed-ID: 19451149  |  Reference-DOI: 10.1093/JB/MVP075
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BUD EMERGENCE PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGEX
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 477-551
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SUPPRESSOR OF RHO3 PROTEIN 1
 
Molecule 2 - CELL DIVISION CONTROL PROTEIN 24
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGEX
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 761-854
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CALCIUM REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KFK)

(-) Sites  (0, 0)

(no "Site" information available for 2KFK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KFK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KFK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KFK)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PB1PS51745 PB1 domain profile.BEM1_YEAST478-551  1A:5-78
CDC24_YEAST761-854  1B:104-186

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YAL041W1YAL041W.1I:62841-654052565CDC24_YEAST1-8548541B:101-186 (gaps)97
2.1YBR200W1YBR200W.1II:620867-6225221656BEM1_YEAST1-5515511A:1-7878

(-) 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:78
 aligned with BEM1_YEAST | P29366 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:78
                                   483       493       503       513       523       533       543        
           BEM1_YEAST   474 SGLKTTKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDTDNFKLQTKLFDGSGEEIKTDSQVSNIIQAKLKISVHDI 551
               SCOP domains d2kfka_ A: automated matches                                                   SCOP domains
               CATH domains 2kfkA00 A:1-78  [code=3.10.20.240, no name defined]                            CATH domains
               Pfam domains ----PB1-2kfkA01 A:5-78                                                         Pfam domains
         Sec.struct. author .....eeeeeee..eeeeeee....hhhhhhhhhh.......eeeee...........hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PB1  PDB: A:5-78 UniProt: 478-551                                          PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-78 UniProt: 1-551 [INCOMPLETE]                              Transcript 2
                 2kfk A   1 PHMKTTKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDTDNFKLQTKLFDGSGEEIKTDSQVSNIIQAKLKISVHDI  78
                                    10        20        30        40        50        60        70        


Chain B from PDB  Type:PROTEIN  Length:86
 aligned with CDC24_YEAST | P11433 from UniProtKB/Swiss-Prot  Length:854

    Alignment length:97
                                   767       777       787       797       807       817       827       837       847       
          CDC24_YEAST   758 PESSILFRISYNNNSNNTSSSEIFTLLVEKVWNFDDLIMAINSKISNTHNNNISPITKIKYQDEDGDFVVLGSDEDWNVAKEMLAENNEKFLNIRLY 854
               SCOP domains d2kfkb_ B: a        utomated matches                                                              SCOP domains
               CATH domains 2kfkB00 B:10        1-186  [code=3.10.20.240, no    name defined]                                 CATH domains
               Pfam domains --------------------PB1-2kfkB01 B:113-185        ---                                            - Pfam domains
         Sec.struct. author ...eeeeeeee.--------...eeeeee...hhhhhhhhhhhhhhhhh---......eeee.....eeee.hhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PB1  PDB: B:104-186 UniProt: 761-854                                                           PROSITE
               Transcript 1 Exon 1.1  PDB: B:101-186 (gaps) UniProt: 1-854 [INCOMPLETE]                                       Transcript 1
                 2kfk B 101 PLGSILFRISYN--------SEIFTLLVEKVWNFDDLIMAINSKISNTH---ISPITKIKYQDEDGDFVVLGSDEDWNVAKEMLAENNEKFLNIRLY 186
                                   110 |       -|      122       132        |-  |    149       159       169       179       
                                     112      113                         141 142
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (24, 29)

NMR Structure(hide GO term definitions)
Chain A   (BEM1_YEAST | P29366)
molecular function
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0032266    phosphatidylinositol-3-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
    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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0000753    cell morphogenesis involved in conjugation with cellular fusion    The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation cellular fusion.
cellular component
    GO:0005935    cellular bud neck    The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
    GO:0005934    cellular bud tip    The end of a cellular bud distal to the site of attachment to the mother cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0000131    incipient cellular bud site    The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
    GO:0030427    site of polarized growth    Any part of a cell where non-isotropic growth takes place.

Chain B   (CDC24_YEAST | P11433)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. 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:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. 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: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).
biological process
    GO:0000282    cellular bud site selection    The specification of the site where a daughter cell will form, in organisms that reproduce by budding. An example of this process is found in Saccharomyces cerevisiae.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0072697    protein localization to cell cortex    A process in which a protein is transported to, or maintained in, the cell cortex.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0007096    regulation of exit from mitosis    Any process involved in the progression from anaphase/telophase to G1 that is associated with a conversion from high to low mitotic CDK activity.
    GO:0031106    septin ring organization    Control of the formation, spatial distribution, and breakdown of the septin ring.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005935    cellular bud neck    The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
    GO:0005934    cellular bud tip    The end of a cellular bud distal to the site of attachment to the mother cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000131    incipient cellular bud site    The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
    GO:0043332    mating projection tip    The apex of the mating projection in unicellular fungi exposed to mating pheromone; site of polarized growth.
    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
        BEM1_YEAST | P29366: 1ip9 1ipg 2czo 2rqv 2rqw 2v6v
        CDC24_YEAST | P11433: 1pqs 1q1o 1tz1 2kfj

(-) Related Entries Specified in the PDB File

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