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 :  PUTATIVE RNA METHYLTRANSFERASE FROM YERSINIA PESTIS IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE.
 
Authors :  J. Osipiuk, N. Maltseva, S. Peterson, W. F. Anderson, A. Joachimiak
Date :  21 May 10  (Deposition) - 23 Jun 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Methyltransferase, S-Adenosyl-L-Homocysteine, Center For Structural Genomics Of Infectious Diseases, Csgid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, N. Maltseva, S. Peterson, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of Putative Rna Methyltransferase From Yersinia Pestis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RNA METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CSPR, YPO0071, YP_0071
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:83 , THR A:84 , THR A:85 , PHE A:104 , GLY A:105 , PRO A:106 , GLU A:107 , THR A:108 , GLY A:110 , ILE A:125 , ILE A:127 , MET A:129 , SER A:135 , MET A:136 , LEU A:138 , HOH A:170 , HOH A:178BINDING SITE FOR RESIDUE SAH A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N4K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:33 -Pro A:34
2Lys B:33 -Pro B:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N4K)

(-) Exons   (0, 0)

(no "Exon" information available for 3N4K)

(-) 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:163
 aligned with TRML_YERPE | Q74Y93 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:163
                              1                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   
           TRML_YERPE     - --MLNIVLFEPEIPPNTGNIIRLCANTGCQLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHDYQAFLDSEKLDSTQPARLFALTTKGTPAHSAVSYQANDYLLFGPETRGLPAYILDALPAQQKIRIPMQADSRSMNLSNAVSVVVYEAWRQLGYPGALLK 161
               SCOP domains d3n4ka_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhh.........eeee......hhhhh......eeee.......hhhhhhh.hhh.ee...........hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4k A  -1 NAMLNIVLFEPEIPPNTGNIIRLCANTGCQLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHDYQAFLDSEKLDSTQPARLFALTTKGTPAHSAVSYQANDYLLFGPETRGLPAYILDALPAQQKIRIPMQADSRSMNLSNAVSVVVYEAWRQLGYPGALLK 161
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with TRML_YERPE | Q74Y93 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           TRML_YERPE     - --MLNIVLFEPEIPPNTGNIIRLCANTGCQLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHDYQAFLDSEKLDSTQPARLFALTTKGTPAHSAVSYQANDYLLFGPETRGLPAYILDALPAQQKIRIPMQADSRSMNLSNAVSVVVYEAWRQLGYPGAL 159
               SCOP domains d3n4kb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --SpoU_methylase-3n4kB01 B:1-147                                                                                                                     ------------ Pfam domains (1)
           Pfam domains (2) --SpoU_methylase-3n4kB02 B:1-147                                                                                                                     ------------ Pfam domains (2)
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhh.........eeee......hhhhh.....eeeee.......hhhhhhhhhhh.ee...........hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4k B  -1 NAMLNIVLFEPEIPPNTGNIIRLCANTGCQLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHDYQAFLDSEKLDSTQPARLFALTTKGTPAHSAVSYQANDYLLFGPETRGLPAYILDALPAQQKIRIPMQADSRSMNLSNAVSVVVYEAWRQLGYPGAL 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N4K)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRML_YERPE | Q74Y93)
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/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
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:33 - Pro A:34   [ RasMol ]  
    Lys B:33 - Pro B:34   [ 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
  3n4k
    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_YERPE | Q74Y93
    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)
  (no 'Enzyme Classificator' available)
    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_YERPE | Q74Y93
    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_YERPE | Q74Y93: 3n4j

(-) Related Entries Specified in the PDB File

3n4j PUTATIVE RNA METHYLTRANSFERASE FROM YERSINIA PESTIS. RELATED ID: IDP90718 RELATED DB: TARGETDB