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(-) Description

Title :  METHANOCOCCUS JANNASCHII FIBRILLARIN PRE-RRNA PROCESSING PROTEIN
 
Authors :  D. C. Boisvert, S. H. Kim
Date :  20 Nov 00  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rrna Processing; Rna Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Boisvert, S. H. Kim
A Structural Approach To Gene Function And Structure Quality For Pyrococcus Horikshii Fibrillarin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 0697
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MET1Mod. Amino AcidMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MET2Mod. Amino AcidMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:56 , LYS A:58 , TYR A:80 , SER A:84 , ALA A:85 , THR A:87 , THR A:88 , PRO A:89 , ASP A:150 , HOH A:517 , HOH A:525BINDING SITE FOR RESIDUE MET A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G8S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:214 -Pro A:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G8S)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRILLARINPS00566 Fibrillarin signature.FLPA_METJA99-113  1A:99-113
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRILLARINPS00566 Fibrillarin signature.FLPA_METJA99-113  2A:99-113

(-) Exons   (0, 0)

(no "Exon" information available for 1G8S)

(-) 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:231
 aligned with FLPA_METJA | Q58108 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:231
                                                                                                                                                                                                                                                               230 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
           FLPA_METJA     1 MEDIKIKEIFENIYEVDLGDGLKRIATKSIVKGKKVYDEKIIKIGDEEYRIWNPNKSKLAAAIIKGLKVMPIKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGMIAIKARSIDVTKDPKEIFKEQKEILEAGGFKIVDEVDIEPFEKDHVMFVGIWEGK-   -
               SCOP domains d1g8sa_ A: Fibrillarin homologue                                                                                                                                                                                                        SCOP domains
               CATH domains -1g8sA01 A:2-52 Phosphorylase Kinase; domain 1      1g8sA02 A:53-230 Vaccinia Virus protein VP39                                                                                                                                      - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeee......eeeee............eeee..eeeee.....hhhhhhhhh...........eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh.....eeeee....hhhhhh.....eeeeee.....hhhhhhhhhhhhheeeeeeeeeeee.hhh....hhhhhhhhhhhhhhhhheeeeeeee.......eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------FIBRILLARIN    ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8s A   1 MEDIKIKEIFENIYEVDLGDGLKRIATKSIVKGKKVYDEKIIKIGDEEYRIWNPNKSKLAAAIIKGLKVMPIKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGMIAIKARSIDVTKDPKEIFKEQKEILEAGGFKIVDEVDIEPFEKDHVMFVGIWEGKM 500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230|
                                                                                                                                                                                                                                                               230|
                                                                                                                                                                                                                                                                500
   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)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G8S)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (FLPA_METJA | Q58108)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:1990259    histone-glutamine methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
    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:0000494    box C/D snoRNA 3'-end processing    Any process involved in forming the mature 3' end of a box C/D snoRNA molecule.
    GO:1990258    histone glutamine methylation    The modification of a histone by addition of a methyl group to an glutamine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0031428    box C/D snoRNP complex    A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
    GO:0032040    small-subunit processome    A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FLPA_METJA | Q58108: 1fbn

(-) Related Entries Specified in the PDB File

1fbn 1FBN IS THE SAME PROTEIN BUT WITHOUT A REFINED METHIONINE AS PART OF THE STRUCTURE
1g8a 1G8A CONTAINS THE SAME PROTEIN BUT FROM A DIFFERENT SOURCE