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(-) Description

Title :  STRUCTURE OF YIBK FROM HAEMOPHILUS INFLUENZAE (HI0766): A METHYLTRANSFERASE WITH A COFACTOR BOUND AT A SITE FORMED BY A KNOT
 
Authors :  K. Lim, H. Zhang, A. Tempczyk, N. Bonander, J. Toedt, A. Howard, E. Eisenstein, O. Herzberg, Structure 2 Function Project (S2F)
Date :  02 Oct 02  (Deposition) - 25 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Methyltransferase, S-Adenosylhomocysteine, Spou Family, Structure 2 Function Project, S2F, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Lim, H. Zhang, A. Tempczyk, W. Krajewski, N. Bonander, J. Toedt, A. Howard, E. Eisenstein, O. Herzberg
Structure Of The Yibk Methyltransferase From Haemophilus Influenzae (Hi0766): A Cofactor Bound At A Site Formed By A Knot
Proteins V. 51 56 2003
PubMed-ID: 12596263  |  Reference-DOI: 10.1002/PROT.10323
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE HI0766
    ChainsA
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET17B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneHI0766
    Organism ScientificHAEMOPHILUS INFLUENZAE
    Organism Taxid727
    SynonymYIBK

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1IOD1Ligand/IonIODIDE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:131BINDING SITE FOR RESIDUE IOD A 2001
2AC2SOFTWARELEU A:78 , THR A:79 , THR A:80 , PHE A:99 , GLY A:100 , PRO A:101 , GLU A:102 , ARG A:104 , GLY A:105 , ARG A:121 , ILE A:122 , MET A:124 , SER A:130 , MET A:131 , SER A:136 , HOH A:1002BINDING SITE FOR RESIDUE SAH A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:33 -Pro A:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MXI)

(-) Exons   (0, 0)

(no "Exon" information available for 1MXI)

(-) 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:156
 aligned with TRML_HAEIN | P44868 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
           TRML_HAEIN     1 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNL 156
               SCOP domains d1mxia_ A: Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue)                                                                                   SCOP domains
               CATH domains 1mxiA00 A:1-156  [code=3.40.1280.10, no name defined]                                                                                                        CATH domains
               Pfam domains SpoU_methylase-1mxiA01 A:1-142                                                                                                                -------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhh...hhhhh...eee.hhhhhhhhhh..eeeee......hhhhh.....eeeee.......hhhhhhhhhhh.ee...........hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mxi A   1 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNL 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRML_HAEIN | P44868)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008175    tRNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA 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:0001510    RNA methylation    Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    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.
    GO:0002131    wobble position cytosine ribose methylation    The process in which the ribose of cytidine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.
    GO:0002132    wobble position uridine ribose methylation    The process in which the ribose of uridine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRML_HAEIN | P448681j85

(-) Related Entries Specified in the PDB File

1j85 1J85 IS YIBK METHYLTRANSFERASE FROM HAEMOPHILIUS INFLUENZAE (HI0766), APO-METHYLTRANSFERASE WITH A KNOT-CONTAINING FOLD RELATED ID: HI0766 RELATED DB: TARGETDB