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(-) Description

Title :  MINIMAL RECOGNITION COMPLEX BETWEEN PRMA AND RIBOSOMAL PROTEIN L11
 
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 :  1.37
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (1x)
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
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21 (DE3) STAR
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: PRMA
    Organism Scientific: THERMUS THERMOPHILUS
    Strain: HB8
    Synonym: L11 MTASE
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L11
    Chains: B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: RPLK, RPL11
    Organism Scientific: THERMUS THERMOPHILUS
    Strain: HB8

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:2 , LYS B:3 , THR B:58 , TYR B:60 , THR B:66 , HOH B:77BINDING SITE FOR RESIDUE EDO B 73
2AC2SOFTWAREARG A:26 , HOH A:110 , ALA B:17 , THR B:18 , ALA B:20 , PRO B:21 , HOH B:101BINDING SITE FOR RESIDUE EDO B 74
3AC3SOFTWARETRP A:2 , ALA A:41 , GLU A:53 , HOH A:69 , GLU B:36 , ALA B:40BINDING SITE FOR RESIDUE EDO B 75

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met B:1 -Lys B:2
2Pro B:21 -Pro B:22
3Thr B:71 -Pro B:72
4Pro C:21 -Pro C:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CJS)

(-) 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:58
 aligned with PRMA_THET8 | Q84BQ9 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:59
                                    10        20        30        40        50         
            PRMA_THET8    1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDEDW 59
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeee..eeeeee..........eeee....-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  3cjs A  1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDE-W 59
                                    10        20        30        40        50      | |
                                                                                   57 |
                                                                                     59


Chain B from PDB  Type:PROTEIN  Length:72
 aligned with RL11_THETH | P36238 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:72
                                    10        20        30        40        50        60        70  
            RL11_THETH    1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTKTP 72
               SCOP domains d3cjsb1 B:1-70 Ribosomal protein L11, N-terminal domain               -- SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee........hhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  3cjs B  1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTKTP 72
                                    10        20        30        40        50        60        70  


Chain C from PDB  Type:PROTEIN  Length:68
 aligned with RL11_THETH | P36238 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:68
                                    12        22        32        42        52        62        
            RL11_THETH    3 KVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTK 70
               SCOP domains d3cjsc1 C:3-70 Ribosomal protein L11, N-terminal domain              SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee........hhhhhhhh...hhhhhhhhhhhhhh.....eeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3cjs C  3 KVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTK 70
                                    12        22        32        42        52        62
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric 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,C   (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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  RL11_THETH | P36238
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRMA_THET8 | Q84BQ9: 1ufk 2nxc 2nxe 2nxj 2nxn 2zbp 2zbq 2zbr 3cjq 3cjr 3cjt 3egv
        RL11_THETH | P36238: 2e34 2e35 2e36 2h8w 2klm 2nxn 3cjq 3cjr 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)
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
3cjr RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH RIBOSOMAL PROTEIN L11 (K39A) AND INHIBITOR SINEFUNGIN.
3cjt
3cju