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(-) Description

Title :  STRUCTURE OF AN ANTIBIOTIC RELATED METHYLTRANSFERASE
 
Authors :  J. Sivaraman, N. Husain
Date :  02 Oct 10  (Deposition) - 17 Nov 10  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Methyltransferase, Transferase, Npma (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Husain, S. Obranic, L. Koscinski, J. Seetharaman, F. Babic, J. M. Bujnicki, G. Maravic-Vlahovicek, J. Sivaraman
Structural Basis For The Methylation Of A1408 In 16S Rrna B A Panaminoglycoside Resistance Methyltransferase Npma From Clinical Isolate And Analysis Of The Npma Interactions With The 30S Ribosomal Subunit.
Nucleic Acids Res. V. 39 1903 2011
PubMed-ID: 21062819  |  Reference-DOI: 10.1093/NAR/GKQ1033

(-) Compounds

Molecule 1 - 16S RRNA METHYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NPMA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SAM4Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:32 , THR A:33 , GLY A:34 , ASN A:38 , ASP A:55 , PRO A:56 , ALA A:87 , GLU A:88 , LEU A:104 , PHE A:105 , TRP A:107 , THR A:109 , LEU A:110 , TYR A:113 , SER A:195 , TRP A:197 , HOH A:226BINDING SITE FOR RESIDUE SAM A 6735
2AC2SOFTWAREGLY B:32 , THR B:33 , 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:227BINDING SITE FOR RESIDUE SAM B 6735
3AC3SOFTWAREPHE B:203 , GLY C:32 , THR C:33 , GLY C:34 , ASN C:38 , ASP C:55 , PRO C:56 , ALA C:86 , ALA C:87 , GLU C:88 , LEU C:104 , PHE C:105 , TRP C:107 , THR C:109 , LEU C:110 , TYR C:113 , SER C:195 , TRP C:197BINDING SITE FOR RESIDUE SAM C 6735
4AC4SOFTWAREPHE A:203 , GLY D:32 , THR D:33 , GLY D:34 , ASN D:38 , ASP D:55 , PRO D:56 , VAL D:57 , ALA D:86 , ALA D:87 , GLU D:88 , LEU D:104 , PHE D:105 , TRP D:107 , THR D:109 , LEU D:110 , TYR D:113 , SER D:195 , TRP D:197BINDING SITE FOR RESIDUE SAM D 6735

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P2K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:116 -Pro A:117
2Lys B:116 -Pro B:117
3Lys C:116 -Pro C:117
4Lys D:116 -Pro D:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P2K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P2K)

(-) Exons   (0, 0)

(no "Exon" information available for 3P2K)

(-) 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:197
 aligned with NPMA_ECOLX | A8C927 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           NPMA_ECOLX     2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee..hhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh.hhhhh....eeee.......hhhhh..eeeeeee..hhhhhhhhhh.hhhhhhhhhhheeeeeeeeeee..------------------hhhhhhhhhhhhhhh...eeeeeeeehhhhhhhh.hhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2k A   2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTY------------------KAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         -       161       171       181       191       201       211     
                                                                                                                                                                     141                160                                                        


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with NPMA_ECOLX | A8C927 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           NPMA_ECOLX     2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee..hhhhhhhhhhh..eeeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.hhhhh....eeee.......hhhhh..eeeeeee...hhhhhhhhh.hhhhhhhhhh.eeeeeeeeeeee.------------------.....hhhhhhhhhh...eeeeeeeeehhhhh...hhhhhhhhh....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2k B   2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTY------------------KAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         -       161       171       181       191       201       211     
                                                                                                                                                                     141                160                                                        


Chain C from PDB  Type:PROTEIN  Length:197
 aligned with NPMA_ECOLX | A8C927 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           NPMA_ECOLX     2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee..hhhhhhhhhh...eeeeee....hhhhhhhhhh...eeeeeee.hhhhhhhhhh....hhhhh....eeeee.hhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhhhhhhh.eeeeeeeeeee..------------------.....hhhhhhhhhhh..eeeeeeeehhhhhh...hhhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2k C   2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTY------------------KAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         -       161       171       181       191       201       211     
                                                                                                                                                                     141                160                                                        


Chain D from PDB  Type:PROTEIN  Length:197
 aligned with NPMA_ECOLX | A8C927 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           NPMA_ECOLX     2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee..hhhhhhhhhh...eeeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhh..hhhhh....eeee.......hhhhh..eeeeeee..hhhhhhhhhh.hhhhhhhhhh.eeeeeeeeee...------------------hhhhhhhhhhhhhhhhh.eeee..ee..hhhhhh.hhhhhhh.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2k D   2 LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTY------------------KAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         -       161       171       181       191       201       211     
                                                                                                                                                                     141                160
   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  (0, 0)

(no "SCOP Domain" information available for 3P2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P2K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P2K)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        NPMA_ECOLX | A8C927: 3mte 3p2e 3p2i 3pb3 4ox9

(-) Related Entries Specified in the PDB File

3p2e 3p2i