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(-) Description

Title :  A CRUCIAL ROLE FOR HIGH INTRINSIC SPECIFICITY IN THE FUNCTION OF YEAST SH3 DOMAINS
 
Authors :  E. J. Stollar, B. Garcia, A. Chong, J. Forman-Kay, A. Davidson
Date :  12 Jun 08  (Deposition) - 16 Jun 09  (Release) - 13 Oct 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Sh3 Domain, Extended Peptide, 3-10 Helix, Acetylation, Actin-Binding, Cytoplasm, Cytoskeleton, Phosphoprotein, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Stollar, B. Garcia, P. A. Chong, A. Rath, H. Lin, J. D. Forman-Kay, A. R. Davidson
Structural, Functional, And Bioinformatic Studies Demonstrate The Crucial Role Of An Extended Peptide Binding Site For The Sh3 Domain Of Yeast Abp1P
J. Biol. Chem. V. 284 26918 2009
PubMed-ID: 19590096  |  Reference-DOI: 10.1074/JBC.M109.028431
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACTIN-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector: PET32A
    Expression System Vector Type: VECTOR
    Fragment: SH3 DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ABP1P
 
Molecule 2 - ACTIN-REGULATING KINASE 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector: PET32A
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 605-621
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 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 2RPN)

(-) Sites  (0, 0)

(no "Site" information available for 2RPN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RPN)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR088W1YCR088W.1III:265065-2668431779ABP1_YEAST1-5925921A:1-5959

(-) 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:59
 aligned with ABP1_YEAST | P15891 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:59
                                   543       553       563       573       583         
           ABP1_YEAST   534 NPWATAEYDYDAAEDNELTFVENDKIINIEFVDDDWWLGELEKDGSKGLFPSNYVSLGN 592
               SCOP domains d2rpna_ A: automated matches                                SCOP domains
               CATH domains 2rpnA00 A:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----SH3_1-2rpnA01 A:5-52                            ------- Pfam domains
         Sec.struct. author ...eee...ee.......ee....eeeeee.....eeeee........eee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-59 UniProt: 1-592 [INCOMPLETE]           Transcript 1
                 2rpn A   1 APWATAEYDYDAAEDNELTFVENDKIINIEFVDDDWWLGELEKDGSKGLFPSNYVSLGN  59
                                    10        20        30        40        50         


Chain B from PDB  Type:PROTEIN  Length:18
 aligned with ARK1_YEAST | P53974 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:18
                                   613        
           ARK1_YEAST   604 DKKTKPTPPPKPSHLKPK 621
               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
                 2rpn B   7 AKKTKPTPPPKPSHLKPK -10
                            ||||||||-2||||||||
                            7|||||||-2||||||||
                             6|||||||-3|||||||
                              5|||||| -4||||||
                               4|||||  -5|||||
                                3||||   -6||||
                                 2|||    -7|||
                                  1||     -8||
                                   0|      -9|
                                   -1      -10
   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: SH3 (175)

(-) Gene Ontology  (21, 26)

NMR Structure(hide GO term definitions)
Chain A   (ABP1_YEAST | P15891)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    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:0000147    actin cortical patch assembly    Assembly of an actin cortical patch, a discrete actin-containing structure found at the plasma membrane of fungal cells.
    GO:0051016    barbed-end actin filament capping    The binding of a protein or protein complex to the barbed (or plus) end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
cellular component
    GO:0030479    actin cortical patch    An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain B   (ARK1_YEAST | P53974)
molecular function
    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:0000147    actin cortical patch assembly    Assembly of an actin cortical patch, a discrete actin-containing structure found at the plasma membrane of fungal cells.
    GO:0007015    actin filament 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. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
cellular component
    GO:0030479    actin cortical patch    An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ABP1_YEAST | P15891: 1hqz 1jo8 2k3b

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