Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) 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
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HI0766
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: YIBK

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric 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
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:33 - Pro A:34   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1mxi
    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
  TRML_HAEIN | P44868
    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
  TRML_HAEIN | P44868
    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
        TRML_HAEIN | P44868: 1j85

(-) 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