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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030-N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S-ADENOSYLMETHIONINE (ADOMET)
 
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 :  2.00
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
    Chains: A, B
    EC Number: 2.1.1.266
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEXP5-CT/TOPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: SPECIFICALLY MONOMETHYLATES THE ADENINE IN POSITION 2030 OF 23S RRNA
    Strain: K-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, 34)

Asymmetric Unit (5, 34)
No.NameCountTypeFull Name
1EDO27Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4SAM2Ligand/IonS-ADENOSYLMETHIONINE
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 18)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:2 , TYR A:4 , HIS A:6 , LYS A:18 , HIS A:19 , THR A:41 , HIS A:42 , ALA A:43 , GLY A:44 , GLY A:99 , SER A:100 , GLU A:118 , LEU A:119 , HIS A:120 , ALA A:142 , ASP A:143 , GLY A:144 , ASP A:164 , HOH A:2002 , HOH A:2007 , HOH A:2058 , HOH A:2059BINDING SITE FOR RESIDUE SAM A1281
02AC2SOFTWARELYS A:30 , LEU A:106 , LEU A:107 , LEU A:108 , ARG A:109 , HOH A:2120 , HOH A:2239 , HOH A:2240 , ARG B:90BINDING SITE FOR RESIDUE GOL A1282
03AC3SOFTWAREVAL A:199 , LEU A:200 , ARG A:201 , ASP A:229 , SER A:230 , HOH A:2192 , HOH A:2195BINDING SITE FOR RESIDUE PEG A1283
04AC4SOFTWAREHIS A:13 , MET A:235 , EDO A:1285 , HOH A:2066 , HOH A:2067BINDING SITE FOR RESIDUE EDO A1284
05AC5SOFTWAREHIS A:13 , GLU A:63 , EDO A:1284 , HOH A:2020 , HOH A:2071 , HOH A:2072BINDING SITE FOR RESIDUE EDO A1285
06AC6SOFTWAREVAL A:226 , LEU A:227 , VAL A:265 , ALA A:267 , THR A:269 , HOH A:2231BINDING SITE FOR RESIDUE EDO A1286
07AC7SOFTWAREHIS A:6 , HIS A:9 , ASN A:12 , ALA A:14 , ASP A:15 , MET A:235 , HOH A:2004 , HOH A:2023BINDING SITE FOR RESIDUE EDO A1287
08AC8SOFTWAREARG A:201 , GLU A:223 , HIS A:271 , THR A:273BINDING SITE FOR RESIDUE EDO A1288
09AC9SOFTWAREPRO A:228 , ASP A:229 , GLY A:270 , HIS A:271BINDING SITE FOR RESIDUE EDO A1289
10BC1SOFTWAREARG A:128 , PHE A:131 , GLN A:132 , VAL A:139 , HOH A:2139 , HOH A:2141BINDING SITE FOR RESIDUE EDO A1290
11BC2SOFTWARETHR A:189 , ILE A:191 , ASN A:244 , PRO A:245 , SO4 A:1297 , HOH A:2241BINDING SITE FOR RESIDUE EDO A1291
12BC3SOFTWAREPHE A:145 , ALA A:175 , HOH A:2150 , HOH A:2178BINDING SITE FOR RESIDUE EDO A1292
13BC4SOFTWARESER A:3 , TYR A:4 , GLU A:168 , HOH A:2167BINDING SITE FOR RESIDUE EDO A1293
14BC5SOFTWARESER A:7 , ALA A:45 , ARG A:47 , TYR A:48 , GLN A:49 , LEU A:126 , HOH A:2135BINDING SITE FOR RESIDUE EDO A1294
15BC6SOFTWAREPRO A:246 , TRP A:247 , LEU A:249 , GLU A:250 , TRP A:276 , HOH A:2218 , HOH A:2219BINDING SITE FOR RESIDUE EDO A1295
16BC7SOFTWAREARG A:95 , LYS A:149 , ALA A:150 , LYS A:151 , LEU A:152 , PRO A:153 , HOH A:2113BINDING SITE FOR RESIDUE EDO A1296
17BC8SOFTWARELEU A:29 , LYS A:32 , ARG A:158 , EDO A:1291 , HOH A:2037 , HOH A:2162 , HOH A:2241BINDING SITE FOR RESIDUE SO4 A1297
18BC9SOFTWAREARG A:47 , HIS A:87 , PHE A:88 , HOH A:2101 , HOH A:2117 , HOH A:2243 , HIS B:87 , ARG B:105BINDING SITE FOR RESIDUE SO4 A1298
19CC1SOFTWARELYS B:18 , HIS B:19 , THR B:41 , HIS B:42 , ALA B:43 , GLY B:44 , GLY B:99 , SER B:100 , GLU B:118 , LEU B:119 , HIS B:120 , ALA B:142 , ASP B:143 , GLY B:144 , ASP B:164 , HOH B:2016 , HOH B:2038 , HOH B:2039 , HOH B:2094BINDING SITE FOR RESIDUE SAM B1281
20CC2SOFTWAREMET B:169 , THR B:171 , ASP B:172 , EDO B:1286BINDING SITE FOR RESIDUE PEG B1282
21CC3SOFTWAREARG B:201 , ILE B:208 , GLN B:221 , EDO B:1296 , HOH B:2139 , HOH B:2188 , HOH B:2189BINDING SITE FOR RESIDUE EDO B1283
22CC4SOFTWAREPRO B:228 , ASP B:229 , GLY B:270 , HIS B:271 , HOH B:2140 , HOH B:2190BINDING SITE FOR RESIDUE EDO B1284
23CC5SOFTWAREALA B:66 , TRP B:69 , EDO B:1289 , HOH B:2132 , HOH B:2191BINDING SITE FOR RESIDUE EDO B1285
24CC6SOFTWAREPHE B:145 , PRO B:165 , PRO B:166 , ASP B:172 , PEG B:1282 , HOH B:2037BINDING SITE FOR RESIDUE EDO B1286
25CC7SOFTWARETHR B:214 , GLY B:215 , ILE B:216 , HOH B:2060 , HOH B:2147BINDING SITE FOR RESIDUE EDO B1287
26CC8SOFTWAREARG B:158BINDING SITE FOR RESIDUE EDO B1288
27CC9SOFTWARETYR B:61 , LEU B:62 , ALA B:66 , LEU B:94 , PRO B:153 , ARG B:186 , EDO B:1285 , HOH B:2049 , HOH B:2051BINDING SITE FOR RESIDUE EDO B1289
28DC1SOFTWARETRP B:247 , GLU B:250 , TRP B:276 , HOH B:2164BINDING SITE FOR RESIDUE EDO B1290
29DC2SOFTWAREALA B:76 , GLU B:77 , GLU B:79 , ALA B:80 , HOH B:2020BINDING SITE FOR RESIDUE EDO B1291
30DC3SOFTWAREHIS B:261 , SER B:262 , VAL B:265 , GLY B:268 , HOH B:2179 , HOH B:2193BINDING SITE FOR RESIDUE EDO B1292
31DC4SOFTWAREPHE B:145 , LYS B:149 , SER B:178 , GLY B:179 , GLU B:182 , HOH B:2122 , HOH B:2194BINDING SITE FOR RESIDUE EDO B1293
32DC5SOFTWAREALA B:181 , THR B:214 , HOH B:2124BINDING SITE FOR RESIDUE EDO B1294
33DC6SOFTWAREASN B:255BINDING SITE FOR RESIDUE EDO B1295
34DC7SOFTWAREHOH A:2170 , ILE B:208 , GLU B:212 , GLN B:221 , EDO B:1283 , HOH B:2188 , HOH B:2189BINDING SITE FOR RESIDUE EDO B1296

(-) SS Bonds  (0, 0)

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

(-) 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 4BLV)

(-) 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 4BLV)

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

    Alignment length:280
                                    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       270       280
           RLMJ_ECOLI     1 MLSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGSEHAERTGEYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARLLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGIYALWYPVVLRQQIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPWLHSKLVPAGTGHATVSWIVPE 280
               SCOP domains d4blva_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh...hhhhhhhhhhhhhhhhhhh......eeee......eee..hhhhhhh.hhhh.hhh.......hhhhhhhhhhhhhh.......eeehhhhhhhhhh....eeeee....hhhhhhhhhh.....eeee..hhhhhhhhh.......eeeee.......hhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh.....eeeeeee...........eeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------N6_MTAS--------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4blv A   1 MLSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLGSEHAERTGEYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARLLLREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGIYALWYPVVLRQQIKRMIHDLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPWLHSKLVPAGTGHATVSWIVPE 280
                                    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       270       280


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 d4blvb_ B: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh......eeee......eee...---....hhhh.hhh.......hhhhhhhhhhhhhh.......eeehhhhhhhhhh....eeeee.....hhhhhhhhh.....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
                 4blv 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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BLV)

(-) Pfam Domains  (0, 0)

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

(-) 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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    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RLMJ_ECOLI | P37634
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RLMJ_ECOLI | P37634: 4blu 4blw

(-) Related Entries Specified in the PDB File

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