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(-) Description

Title :  2.1 ANGSTROM CRYSTAL STRUCTURE OF THE L114P MUTANT OF E. COLI KSGA
 
Authors :  J. N. Scarsdale, F. N. Musayev, J. P. Rife
Date :  08 Sep 11  (Deposition) - 15 Feb 12  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rrna Adenine Dimethyltransferase, Ribogenesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. C. O'Farrell, F. N. Musayev, J. N. Scarsdale, J. P. Rife
Control Of Substrate Specificity By A Single Active Site Residue Of The Ksga Methyltransferase.
Biochemistry V. 51 466 2012
PubMed-ID: 22142337  |  Reference-DOI: 10.1021/BI201539J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A
    ChainsA, B
    EC Number2.1.1.182
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneB0051, JW0050, KSGA, RSMA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymECKSGA, 16S RRNA (ADENINE(1518)-N(6)/ADENINE(1519)-N(6))- DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLADENOSINE TRANSFERASE, 16S RRNA DIMETHYLASE, HIGH LEVEL KASUGAMYCIN RESISTANCE PROTEIN KSGA, KASUGAMYCIN DIMETHYLTRANSFERASE, S-ADENOSYLMETHIONINE-6-N', N'- ADENOSYL(RRNA) DIMETHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:158 , ARG A:159 , HOH A:297BINDING SITE FOR RESIDUE CL A 274
2AC2SOFTWAREARG A:74 , HOH A:280 , ARG B:74BINDING SITE FOR RESIDUE CL A 275
3AC3SOFTWAREARG B:147 , GLY B:158 , ARG B:159 , HOH B:286BINDING SITE FOR RESIDUE PO4 B 274

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:182 -Pro A:183
2Thr B:182 -Pro B:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_ECOLI11-268  1B:11-267
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_ECOLI41-68
 
  2A:41-68
B:41-68
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_ECOLI11-268  0-
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_ECOLI41-68
 
  1A:41-68
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_ECOLI11-268  1B:11-267
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_ECOLI41-68
 
  1-
B:41-68

(-) Exons   (0, 0)

(no "Exon" information available for 3TPZ)

(-) 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:253
 aligned with RSMA_ECOLI | P06992 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:253
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   
           RSMA_ECOLI    15 FGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAEN 267
               SCOP domains d3tpza_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhh.....eeeee......hhhhhhhh...eeee..hhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SAM_RNA_A_N6_MT  PDB: - UniProt: 11-268                                                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) --------------------------RRNA_A_DIMETH  PDB: A:41-68 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tpz A  15 FGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNPPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAEN 267
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with RSMA_ECOLI | P06992 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:267
                                    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       260       
           RSMA_ECOLI     1 MNNRVHQGHLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAEN 267
               SCOP domains d3tpzb_ B: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......ee.hhhhhhhhhhhhh.....eeeee......hhhhhhh....eeee..hhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhh.......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------SAM_RNA_A_N6_MT  PDB: B:11-267 UniProt: 11-268                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) ----------------------------------------RRNA_A_DIMETH  PDB: B:41-68 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tpz B   1 MNNRVHQGHLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNPPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAEN 267
                                    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       260       

   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 Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RSMA_ECOLI | P06992)
molecular function
    GO:0052908    16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity    Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016433    rRNA (adenine) methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine.
    GO:0000179    rRNA (adenine-N6,N6-)-dimethyltransferase activity    Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA 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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
    GO:0000154    rRNA modification    The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0000028    ribosomal small subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RSMA_ECOLI | P069921qyr 4adv

(-) Related Entries Specified in the PDB File

1qam THE STRUCTURE OF THE RRNA METHYL TRANSFERASE ERMC'
1qyr CRYSTAL STRUCTURE OF E. COLI KSGA
2fyc CRYSTAL STRUCTURE OF DIM1 FROM THE THERMOPHILIC ARCHEON M. JANNASCHI
3ftd CRYSTAL STRUCTURE OF A AEOLICUS KSGA AT 1.44 A RESOLUTION
3fut APO FORM OF T THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P212121
3fyd CRYSTAL STRUCTURE OF DIM1 FROM THE THERMOPHILIC ARCHEON M. JANNASCHI