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4BLV

Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylmethionine (AdoMet)

Functional Information from GO Data
ChainGOidnamespacecontents
A0003676molecular_functionnucleic acid binding
A0003723molecular_functionRNA binding
A0005515molecular_functionprotein binding
A0005829cellular_componentcytosol
A0006364biological_processrRNA processing
A0008168molecular_functionmethyltransferase activity
A0008649molecular_functionrRNA methyltransferase activity
A0008988molecular_functionrRNA (adenine-N6-)-methyltransferase activity
A0015976biological_processcarbon utilization
A0016740molecular_functiontransferase activity
A0032259biological_processmethylation
A0036307molecular_function23S rRNA (adenine(2030)-N(6))-methyltransferase activity
A0070475biological_processrRNA base methylation
B0003676molecular_functionnucleic acid binding
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0005829cellular_componentcytosol
B0006364biological_processrRNA processing
B0008168molecular_functionmethyltransferase activity
B0008649molecular_functionrRNA methyltransferase activity
B0008988molecular_functionrRNA (adenine-N6-)-methyltransferase activity
B0015976biological_processcarbon utilization
B0016740molecular_functiontransferase activity
B0032259biological_processmethylation
B0036307molecular_function23S rRNA (adenine(2030)-N(6))-methyltransferase activity
B0070475biological_processrRNA base methylation
Functional Information from PDB Data
site_idAC1
Number of Residues22
DetailsBINDING SITE FOR RESIDUE SAM A 1281
ChainResidue
ALEU2
AGLY99
ASER100
AGLU118
ALEU119
AHIS120
AALA142
AASP143
AGLY144
AASP164
AHOH2002
ATYR4
AHOH2007
AHOH2058
AHOH2059
AHIS6
ALYS18
AHIS19
ATHR41
AHIS42
AALA43
AGLY44

site_idAC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 1282
ChainResidue
ALYS30
ALEU106
ALEU107
ALEU108
AARG109
AHOH2120
AHOH2239
AHOH2240
BARG90

site_idAC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PEG A 1283
ChainResidue
AVAL199
ALEU200
AARG201
AASP229
ASER230
AHOH2192
AHOH2195

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 1284
ChainResidue
AHIS13
AMET235
AEDO1285
AHOH2066
AHOH2067

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 1285
ChainResidue
AHIS13
AGLU63
AEDO1284
AHOH2020
AHOH2071
AHOH2072

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 1286
ChainResidue
AVAL226
ALEU227
AVAL265
AALA267
ATHR269
AHOH2231

site_idAC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 1287
ChainResidue
AHIS6
AHIS9
AASN12
AALA14
AASP15
AMET235
AHOH2004
AHOH2023

site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 1288
ChainResidue
AARG201
AGLU223
AHIS271
ATHR273

site_idAC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 1289
ChainResidue
APRO228
AASP229
AGLY270
AHIS271

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 1290
ChainResidue
AARG128
APHE131
AGLN132
AVAL139
AHOH2139
AHOH2141

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 1291
ChainResidue
ATHR189
AILE191
AASN244
APRO245
ASO41297
AHOH2241

site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 1292
ChainResidue
APHE145
AALA175
AHOH2150
AHOH2178

site_idBC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 1293
ChainResidue
ASER3
ATYR4
AGLU168
AHOH2167

site_idBC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 1294
ChainResidue
ASER7
AALA45
AARG47
ATYR48
AGLN49
ALEU126
AHOH2135

site_idBC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 1295
ChainResidue
ATRP247
ALEU249
AGLU250
ATRP276
AHOH2218
AHOH2219
APRO246

site_idBC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 1296
ChainResidue
AARG95
ALYS149
AALA150
ALYS151
ALEU152
APRO153
AHOH2113

site_idBC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 A 1297
ChainResidue
ALEU29
ALYS32
AARG158
AEDO1291
AHOH2037
AHOH2162
AHOH2241

site_idBC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 A 1298
ChainResidue
AARG47
AHIS87
APHE88
AHOH2101
AHOH2117
AHOH2243
BHIS87
BARG105

site_idCC1
Number of Residues19
DetailsBINDING SITE FOR RESIDUE SAM B 1281
ChainResidue
BLYS18
BHIS19
BTHR41
BHIS42
BALA43
BGLY44
BGLY99
BSER100
BGLU118
BLEU119
BHIS120
BALA142
BASP143
BGLY144
BASP164
BHOH2016
BHOH2038
BHOH2039
BHOH2094

site_idCC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PEG B 1282
ChainResidue
BMET169
BTHR171
BASP172
BEDO1286

site_idCC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 1283
ChainResidue
BARG201
BILE208
BGLN221
BEDO1296
BHOH2139
BHOH2188
BHOH2189

site_idCC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 1284
ChainResidue
BPRO228
BASP229
BGLY270
BHIS271
BHOH2140
BHOH2190

site_idCC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 1285
ChainResidue
BALA66
BTRP69
BEDO1289
BHOH2132
BHOH2191

site_idCC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 1286
ChainResidue
BPHE145
BPRO165
BPRO166
BASP172
BPEG1282
BHOH2037

site_idCC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 1287
ChainResidue
BTHR214
BGLY215
BILE216
BHOH2060
BHOH2147

site_idCC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO B 1288
ChainResidue
BARG158

site_idCC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO B 1289
ChainResidue
BTYR61
BLEU62
BALA66
BLEU94
BPRO153
BARG186
BEDO1285
BHOH2049
BHOH2051

site_idDC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 1290
ChainResidue
BTRP247
BGLU250
BTRP276
BHOH2164

site_idDC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 1291
ChainResidue
BALA76
BGLU77
BGLU79
BALA80
BHOH2020

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 1292
ChainResidue
BHIS261
BSER262
BVAL265
BGLY268
BHOH2179
BHOH2193

site_idDC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 1293
ChainResidue
BPHE145
BLYS149
BSER178
BGLY179
BGLU182
BHOH2122
BHOH2194

site_idDC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 1294
ChainResidue
BALA181
BTHR214
BHOH2124

site_idDC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO B 1295
ChainResidue
BASN255

site_idDC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 1296
ChainResidue
AHOH2170
BILE208
BGLU212
BGLN221
BEDO1283
BHOH2188
BHOH2189

Functional Information from PROSITE/UniProt
site_idPS00092
Number of Residues7
DetailsN6_MTASE N-6 Adenine-specific DNA methylases signature. ILIDPPY
ChainResidueDetails
AILE161-TYR167
AILE241-TRP247

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"23945937","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23945937","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsSite: {"description":"Interaction with substrate rRNA","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

240971

PDB entries from 2025-08-27

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