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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030-N6)-METHYLTRANSFERASE RLMJ
 
Authors :  A. S. Punekar, J. Liljeruhm, T. R. Shepherd, A. C. Forster, M. Selmer
Date :  04 May 13  (Deposition) - 21 Aug 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, N6-Methyladenine, Rossmann-Like Fold, Subdomain Insertion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. S. Punekar, J. Liljeruhm, T. R. Shepherd, A. C. Forster, M. Selmer
Structural And Functional Insights Into The Molecular Mechanism Of Rrna M6A Methyltransferase Rlmj.
Nucleic Acids Res. V. 41 9537 2013
PubMed-ID: 23945937  |  Reference-DOI: 10.1093/NAR/GKT719

(-) Compounds

Molecule 1 - RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
    ChainsA, B
    EC Number2.1.1.266
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPEXP5-CT/TOPO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    Other DetailsSPECIFICALLY MONOMETHYLATES THE ADENINE IN POSITION 2030 OF 23S RRNA
    StrainK-12

 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  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4SO42Ligand/IonSULFATE ION
5TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (5, 15)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:12 , ASP A:15 , LYS A:18 , ASP A:164 , TRP A:195 , EDO A:1283 , EDO A:1284 , EDO A:1287 , HOH A:2290BINDING SITE FOR RESIDUE TRS A1281
02AC2SOFTWAREARG A:157 , THR A:189 , HOH A:2039 , HOH A:2110 , HOH A:2111 , HOH A:2118 , HOH A:2227BINDING SITE FOR RESIDUE GOL A1282
03AC3SOFTWARESER A:7 , ALA A:10 , ASP A:15 , TYR A:48 , TYR A:97 , PRO A:98 , TRS A:1281 , EDO A:1287 , HOH A:2032BINDING SITE FOR RESIDUE EDO A1283
04AC4SOFTWARELYS A:18 , HIS A:42 , ASP A:164 , TRS A:1281 , HOH A:2030 , HOH A:2074 , HOH A:2199BINDING SITE FOR RESIDUE EDO A1284
05AC5SOFTWAREPRO A:228 , ARG A:233 , THR A:269 , HOH A:2282 , HOH A:2291BINDING SITE FOR RESIDUE EDO A1285
06AC6SOFTWAREASN A:83 , LYS A:86 , HIS A:87 , ARG A:90 , HOH A:2292 , EDO B:1293 , EDO B:1294BINDING SITE FOR RESIDUE EDO A1286
07AC7SOFTWARESER A:7 , HIS A:9 , ALA A:10 , TRS A:1281 , EDO A:1283 , HOH A:2015BINDING SITE FOR RESIDUE EDO A1287
08AC8SOFTWARELEU A:29 , LYS A:32 , ARG A:158 , HOH A:2043 , HOH A:2197 , HOH A:2228 , HOH A:2287 , HOH A:2288 , HOH A:2289BINDING SITE FOR RESIDUE SO4 A1288
09AC9SOFTWAREASN B:12 , ASP B:15 , LYS B:18 , ASP B:164 , TRP B:195 , GOL B:1282 , PEG B:1285 , EDO B:1286 , HOH B:2254 , HOH B:2255 , HOH B:2256BINDING SITE FOR RESIDUE TRS B1281
10BC1SOFTWARELYS B:18 , TYR B:48 , ASP B:164 , TRS B:1281 , EDO B:1286 , HOH B:2051 , HOH B:2054 , HOH B:2257 , HOH B:2258BINDING SITE FOR RESIDUE GOL B1282
11BC2SOFTWAREARG B:67 , TYR B:184 , LYS B:185 , GLY B:215 , HOH B:2175 , HOH B:2178 , HOH B:2181BINDING SITE FOR RESIDUE PEG B1283
12BC3SOFTWARESER B:262 , LYS B:263 , PRO B:266 , HOH B:2243BINDING SITE FOR RESIDUE PEG B1284
13BC4SOFTWARESER B:7 , PHE B:8 , HIS B:9 , TRS B:1281 , HOH B:2254 , HOH B:2256BINDING SITE FOR RESIDUE PEG B1285
14BC5SOFTWARESER B:7 , ALA B:10 , ASP B:15 , TYR B:48 , TYR B:97 , TRS B:1281 , GOL B:1282 , HOH B:2018 , HOH B:2254BINDING SITE FOR RESIDUE EDO B1286
15BC6SOFTWAREPRO B:246 , TRP B:247 , HOH B:2035 , HOH B:2036BINDING SITE FOR RESIDUE EDO B1287
16BC7SOFTWARELYS B:32 , ARG B:158 , HOH B:2260BINDING SITE FOR RESIDUE EDO B1288
17BC8SOFTWAREARG B:109 , GLN B:111 , HOH B:2119 , HOH B:2261BINDING SITE FOR RESIDUE EDO B1289
18BC9SOFTWAREPRO B:166 , GLU B:168 , ASP B:172BINDING SITE FOR RESIDUE EDO B1290
19CC1SOFTWARETHR B:58 , GLU B:182 , LYS B:185 , ARG B:186 , HOH B:2063 , HOH B:2176BINDING SITE FOR RESIDUE EDO B1291
20CC2SOFTWAREARG A:206 , GLU B:250 , SER B:275 , TRP B:276 , HOH B:2252 , HOH B:2262BINDING SITE FOR RESIDUE EDO B1292
21CC3SOFTWAREARG A:90 , EDO A:1286 , LEU B:106 , EDO B:1294 , HOH B:2037BINDING SITE FOR RESIDUE EDO B1293
22CC4SOFTWAREARG A:90 , EDO A:1286 , HOH A:2046 , ARG B:90 , EDO B:1293 , HOH B:2264 , HOH B:2265BINDING SITE FOR RESIDUE EDO B1294
23CC5SOFTWAREHIS A:87 , HOH A:2151 , ARG B:47 , HIS B:87 , PHE B:88 , HOH B:2115BINDING SITE FOR RESIDUE SO4 B1295

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BLU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:152 -Pro A:153
2Leu B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BLU)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.RLMJ_ECOLI161-167
 
241-247
 
  4A:161-167
B:161-167
A:241-247
B:241-247
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.RLMJ_ECOLI161-167
 
241-247
 
  2A:161-167
-
A:241-247
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.RLMJ_ECOLI161-167
 
241-247
 
  2-
B:161-167
-
B:241-247

(-) Exons   (0, 0)

(no "Exon" information available for 4BLU)

(-) 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:279
 aligned with RLMJ_ECOLI | P37634 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271         
           RLMJ_ECOLI     2 LSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGSEHAERTGEYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARLLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGIYALWYPVVLRQQIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPWLHSKLVPAGTGHATVSWIVPE 280
               SCOP domains d4blua_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh......eeee......eee..........hhhh.hhh.......hhhhhhhhhhhhhh.......eeehhhhhhhhhh....eeeee....hhhhhhhhhh.....eeee.....hhhhhh.......eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhh....eeeeeee...........eeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------N6_MTAS--------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4blu A   2 LSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGSEHAERTGEYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARLLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGIYALWYPVVLRQQIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPWLHSKLVPAGTGHATVSWIVPE 280
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271         

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with RLMJ_ECOLI | P37634 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271         
           RLMJ_ECOLI     2 LSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGSEHAERTGEYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARLLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGIYALWYPVVLRQQIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPWLHSKLVPAGTGHATVSWIVPE 280
               SCOP domains d4blub_ B: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh......eeee......eee...---....hhhh.hhh.......hhhhhhhhhhhhhh.......eeehhhhhhhhhh....eeeee....hhhhhhhhhh.....eeee..hhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhh....eeeeeee...........eeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------N6_MTAS--------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4blu B   2 LSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGS---ERTGEYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARLLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGIYALWYPVVLRQQIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPWLHSKLVPAGTGHATVSWIVPE 280
                                    11        21        31        41        51|   |   61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271         
                                                                             52  56                                                                                                                                                                                                                                

   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 4BLU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BLU)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RLMJ_ECOLI | P37634)
molecular function
    GO:0036307    23S rRNA (adenine(2030)-N(6))-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(2030) in 23S rRNA.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008988    rRNA (adenine-N6-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N6-methyladenine.
    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:0015976    carbon utilization    A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism.
    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:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    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
        RLMJ_ECOLI | P376344blv 4blw

(-) Related Entries Specified in the PDB File

4blv CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030- N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S- ADENOSYLMETHIONINE (ADOMET)
4blw CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030- N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S- ADENOSYLHOMOCYSTEINE (ADOHCY) AND ADENOSINE MONOPHOSPHATE ( AMP)