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(-) Description

Title :  RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH RIBOSOMAL PROTEIN L11 (K39A) AND INHIBITOR SINEFUNGIN.
 
Authors :  H. Demirci, S. T. Gregory, A. E. Dahlberg, G. Jogl
Date :  13 Mar 08  (Deposition) - 20 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  S-Adenosyl-L-Methionine Dependent Methyltransferase, Post- Translational Modification, Multi-Specific Trimethylation, Ribonucleoprotein, Ribosomal Protein, Rna-Binding, Rrna-Binding, Transferase-Ribosomal Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Demirci, S. T. Gregory, A. E. Dahlberg, G. Jogl
Multiple-Site Trimethylation Of Ribosomal Protein L11 By Th Prma Methyltransferase.
Structure V. 16 1059 2008
PubMed-ID: 18611379  |  Reference-DOI: 10.1016/J.STR.2008.03.016

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30B
    Expression System StrainBL21 (DE3) STAR
    Expression System Vector TypePLASMID
    GenePRMA
    Organism ScientificTHERMUS THERMOPHILUS
    StrainHB8
    SynonymL11 MTASE
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L11
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Vector TypePLASMID
    GeneRPLK, RPL11
    MutationYES
    Organism ScientificTHERMUS THERMOPHILUS
    StrainHB8

 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
1SFG1Ligand/IonSINEFUNGIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:99 , GLY A:100 , THR A:107 , GLY A:128 , THR A:129 , LEU A:134 , ASP A:149 , ILE A:150 , GLY A:174 , SER A:175 , ASN A:191 , LEU A:192 , HOH A:285 , HOH A:286 , HOH A:314 , HOH A:375 , HOH A:469 , HOH A:473 , HOH A:497BINDING SITE FOR RESIDUE SFG A 255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:73 -Pro A:74
2Gly A:183 -Pro A:184
3Met B:1 -Lys B:2
4Pro B:21 -Pro B:22
5Thr B:71 -Pro B:72
6Met B:134 -Gly B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_THETH125-140  1B:125-137

(-) Exons   (0, 0)

(no "Exon" information available for 3CJR)

(-) 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:249
 aligned with PRMA_THET8 | Q84BQ9 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
           PRMA_THET8     1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDEDWLEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 254
               SCOP domains d3cjra1 A:1-254 PrmA-like protein TTHA0656 (TT0836)                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh..eeee...eeeeee..........eee..-----hhhhhhh...eee..eeee..........eeee...........hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cjr A   1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEV-----LEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 254
                                    10        20        30        40        50   |    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
                                                                                54    60                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with RL11_THETH | P36238 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       
           RL11_THETH     1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVE 137
               SCOP domains d3cjrb2 B:1-70 Ribosomal protein L11, N-terminal domain               d3cjrb1 B                   :71-137 Ribosomal protein L11, C-termin SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee........hhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeee...hhhhhhh-------------------...hhhhhhhhhh...........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11 PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cjr B   1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVAAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIR-------------------ITWEQVLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVE 137
                                    10        20        30        40        50        60        70        |-         -       100       110       120       130       
                                                                                                         79                  99                                      

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CJR)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRMA_THET8 | Q84BQ9)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (RL11_THETH | P36238)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0070180    large ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRMA_THET8 | Q84BQ91ufk 2nxc 2nxe 2nxj 2nxn 2zbp 2zbq 2zbr 3cjq 3cjs 3cjt 3egv
        RL11_THETH | P362382e34 2e35 2e36 2h8w 2klm 2nxn 3cjq 3cjs 3cjt 4v67

(-) Related Entries Specified in the PDB File

1ufk APO-FORM OF T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA)AT 1.9 A RESOLUTION
2nxc APO-FORM OF T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA)AT 1.59 A RESOLUTION
2nxe T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE
2nxj T.THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN SPACE GROUP P 21 21 2
2nxn T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH RIBOSOMAL PROTEIN L11
3cjq RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH DIMETHYLATED RIBOSOMAL PROTEIN L11 IN SPACE GROUP P212121
3cjs
3cjt
3cju