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(-) Description

Title :  THE STRUCTURE OF THE FYR DOMAIN
 
Authors :  M. M. Garcia-Alai, M. D. Allen, A. C. Joerger, M. Bycroft
Date :  01 Dec 09  (Deposition) - 05 May 10  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nucleus, Cell Cycle, Tumor Suppressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Garcia-Alai, M. D. Allen, A. C. Joerger, M. Bycroft
The Structure Of The Fyr Domain Of Transforming Growth Factor Beta Regulator 1 (Tbrg1)(Pna)
Protein Sci. V. 19 1432 2010
PubMed-ID: 20506279  |  Reference-DOI: 10.1002/PRO.404

(-) Compounds

Molecule 1 - TRANSFORMING GROWTH FACTOR BETA REGULATOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector: PRSETA
    Fragment: FYR DOMAIN, RESIDUES 179-324
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR INTERACTOR OF ARF AND MDM2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:269 , LEU A:272 , ARG A:273 , SER A:276 , LEU A:282 , MET A:283 , LEU A:286 , HOH A:2119 , HOH A:2157BINDING SITE FOR RESIDUE GOL A1325
2AC2SOFTWAREPHE A:247 , SER A:263 , ALA A:264 , ASP A:265 , ALA A:291 , PHE A:296 , HOH A:2158 , HOH A:2159 , HOH A:2160BINDING SITE FOR RESIDUE GOL A1326

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FYRNPS51542 FYR domain FYRN motif profile.TBRG1_HUMAN182-241  1A:182-241
2FYRCPS51543 FYR domain FYRC motif profile.TBRG1_HUMAN242-321  1A:242-321
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FYRNPS51542 FYR domain FYRN motif profile.TBRG1_HUMAN182-241  2A:182-241
2FYRCPS51543 FYR domain FYRC motif profile.TBRG1_HUMAN242-321  2A:242-321

(-) Exons   (0, 0)

(no "Exon" information available for 2WZO)

(-) Sequences/Alignments

Asymmetric 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:146
 aligned with TBRG1_HUMAN | Q3YBR2 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:146
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318      
          TBRG1_HUMAN   179 GRPVFPIGLGGLTVYSLGEIITDRPGFHDESAIYPVGYCSTRIYASMKCPDQKCLYTCQIKDGGVQPQFEIVPEDDPQNAIVSSSADACHAELLRTISTTMGKLMPNLLPAGADFFGFSHPAIHNLIQSCPGARKCINYQWVKFDV 324
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------FYRN-2wzoA02 A:187-240                                -FYRC-2wzoA01 A:242-324                                                              Pfam domains
         Sec.struct. author ......eee..eeeeeeee....hhhh........eeeeeeeeee.......eeeeeeeeee....eeeeeee..hhhhheee.hhhhhhhhhhhhhhhhhh........hhhhhhh..hhhhhhhhh...hhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FYRN  PDB: A:182-241 UniProt: 182-241                       FYRC  PDB: A:242-321 UniProt: 242-321                                           --- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wzo A 179 GRPVFPIGLGGLTVYSLGEIITDRPGFHDESAIYPVGYCSTRIYASMKCPDQKCLYTCQIKDGGVQPQFEIVPEDDPQNAIVSSSADACHAELLRTISTTMGKLMPNLLPAGADFFGFSHPAIHNLIQSCPGARKCINYQWVKFDV 324
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318
   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  (0, 0)

(no "SCOP Domain" information available for 2WZO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WZO)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: FYRC] (1)
(-)
Clan: no clan defined [family: FYRN] (1)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (TBRG1_HUMAN | Q3YBR2)
molecular function
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0032066    nucleolus to nucleoplasm transport    The directed movement of substances from the nucleolus to the nucleoplasm.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
cellular component
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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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