Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF S. CEREVISIAE YNR046W, A ZINC FINGER PROTEIN FROM THE ERF1 METHYLTRANSFERASE COMPLEX.
 
Authors :  V. Heurgue-Hamard, M. Graille, N. Scrima, N. Ulryck, S. Champ, H. Van Tilbeurgh, R. H. Buckingham
Date :  27 Sep 06  (Deposition) - 28 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation Termination, Methyltransferase, Transferase, Erf1, Nuclear Protein, Protein Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Heurgue-Hamard, M. Graille, N. Scrima, N. Ulryck, S. Champ, H. Van Tilbeurgh, R. H. Buckingham
The Zinc Finger Protein Ynr046W Is Plurifunctional And A Component Of The Erf1 Methyltransferase In Yeast.
J. Biol. Chem. V. 281 36140 2006
PubMed-ID: 17008308  |  Reference-DOI: 10.1074/JBC.M608571200

(-) Compounds

Molecule 1 - PROTEIN TRM112
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: YIBPC27
    Synonym: YNR046W, TRNA METHYLTRANSFERASE 112

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:11 , CYS A:16 , CYS A:112 , CYS A:115BINDING SITE FOR RESIDUE ZN A1138
2AC2SOFTWAREMET A:1 , LYS A:2 , ARG A:53 , SER A:104 , HIS A:133 , HOH A:2144BINDING SITE FOR RESIDUE EDO A1137

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J6A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:23 -Pro A:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J6A)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNR046W1YNR046W.1XIV:707791-708198408TR112_YEAST1-1351351A:1-135135

(-) Sequences/Alignments

Asymmetric/Biological 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:136
 aligned with TR112_YEAST | P53738 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:136
                                                                                                                                                                135 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    | 
          TR112_YEAST     1 MKFLTTNFLKCSVKACDTSNDNFPLQYDGSKCQLVQDESIEFNPEFLLNIVDRVDWPAVLTVAAELGNNALPPTKPSFPSSIQELTDDDMAILNDLHTLLLQTSIAEGEMKCRNCGHIYYIKNGIPNLLLPPHLV-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhh........ee.....eeee......hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee..ee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-135 UniProt: 1-135                                                                                                  - Transcript 1
                 2j6a A   1 MKFLTTNFLKCSVKACDTSNDNFPLQYDGSKCQLVQDESIEFNPEFLLNIVDRVDWPAVLTVAAELGNNALPPTKPSFPSSIQELTDDDMAILNDLHTLLLQTSIAEGEMKCRNCGHIYYIKNGIPNLLLPPHLVH 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 2J6A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J6A)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TR112_YEAST | P53738)
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).
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    GO:0016435    rRNA (guanine) methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylguanine.
    GO:0004809    tRNA (guanine-N2-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA containing guanine = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine.
biological process
    GO:0000470    maturation of LSU-rRNA    Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
    GO:0030490    maturation of SSU-rRNA    Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule.
    GO:0018364    peptidyl-glutamine methylation    The addition of a methyl group to a glutamine residue in a protein.
    GO:0070476    rRNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an rRNA molecule.
    GO:0042273    ribosomal large subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0042274    ribosomal small subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
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:0035657    eRF1 methyltransferase complex    A protein complex required for the methylation of a glutamine (Gln) residue in the protein release factor eRF1. In S. cerevisiae, this complex consists of at least Trm112p and Mtq2p.
    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:0043528    tRNA (m2G10) methyltransferase complex    A protein complex required for the methylation of the guanosine nucleotide at position 10 (m2G10) in tRNA. In S. cerevisiae, this complex consists of at least two subunits, Trm11p and Trm112p.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:23 - Pro A:24   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2j6a
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TR112_YEAST | P53738
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TR112_YEAST | P53738
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TR112_YEAST | P53738: 4qtt 4qtu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2J6A)