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(-) Description

Title :  CRYSTAL STRUCTURE OF 16S RRNA METHYLTRANFERASE
 
Authors :  R. A. Macmaster, G. L. Conn, N. Zelinskaya
Date :  30 Apr 10  (Deposition) - 08 Dec 10  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, 16S, Ribosomal, Aminoglycoside, Resistance, Rna, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Macmaster, N. Zelinskaya, M. Savic, C. R. Rankin, G. L. Conn
Structural Insights Into The Function Of Aminoglycoside-Resistance A1408 16S Rrna Methyltransferases From Antibiotic-Producing And Human Pathogenic Bacteria.
Nucleic Acids Res. V. 38 7791 2010
PubMed-ID: 20639535  |  Reference-DOI: 10.1093/NAR/GKQ627

(-) Compounds

Molecule 1 - 16S RRNA METHYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET44
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NPMA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: ARS3

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:32 , THR A:33 , GLY A:34 , ASN A:38 , ASP A:55 , PRO A:56 , ASN A:60 , ALA A:86 , ALA A:87 , GLU A:88 , LEU A:104 , PHE A:105 , TRP A:107 , SER A:195 , TRP A:197 , HOH A:222 , HOH A:233 , HOH A:278 , PHE B:203BINDING SITE FOR RESIDUE SAM A 220
2AC2SOFTWAREGLY B:32 , THR B:33 , GLY B:34 , ASN B:38 , ASP B:55 , PRO B:56 , ALA B:86 , ALA B:87 , GLU B:88 , LEU B:104 , PHE B:105 , TRP B:107 , THR B:109 , LEU B:110 , SER B:195 , TRP B:197 , HOH B:226 , HOH B:229 , HOH B:268BINDING SITE FOR RESIDUE SAM B 220

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:116 -Pro A:117
2Lys B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MTE)

(-) 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:219
 aligned with NPMA_ECOLX | A8C927 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           NPMA_ECOLX     1 MLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH 219
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhhhhhhhhh...eeeeee....hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh.hhhhh....eeeee.hhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhhhhhhh.eeeeeeeeeee...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhh...hhhhhhhhhh....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mte A   1 MLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with NPMA_ECOLX | A8C927 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           NPMA_ECOLX     1 MLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH 219
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhhhhhhhhh...eeeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.hhhhh....eeee..hhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhhhhhhh.eeeeeeeeeee......hhhhhhhh.....hhhhhhhhhhhhhhhhhheeeeeeeeehhhhhh...hhhhhhhhh.....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mte B   1 MLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3MTE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NPMA_ECOLX | A8C927)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008176    tRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N7-methylguanine.
    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:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.

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        NPMA_ECOLX | A8C927: 3p2e 3p2i 3p2k 3pb3 4ox9

(-) Related Entries Specified in the PDB File

3mq2