Structure of PDB 7afo Chain Y Binding Site BS01

Receptor Information

>7afo Chain Y (length=252) Species: 562 (Escherichia coli)

QNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIE
LDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPY
NISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQY
YCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTE
AFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAE
NA

Ligand information

>7afo Chain A (length=971)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcgccuugaaaccguaggggaa
ccugcgguuggaucaccuccu

........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<...<<<<<<<..........>>>>.>>>.>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<...
..<<<<<......>>>>>......>>.>.....<<<....>>>....<<<
<<<..<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<.
.<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....
>>>...>>>>>.>>.<<<<<............>>>>>.<<<<....>>>>
...>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>
>>>..<<<<......<<<<....>>>>.....>>>>...<.<<<<<....
..<.<<<<<<<<.......>>>>>>>>.>........>>>>>....>..<
<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>
>>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<
<<<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>
>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>.
.....>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>
>...>>>...>>>>....<<<<<<...<<...<<<<.........>>>>.
..>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>
>>>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<<...
.>>>>....>>>..)))).]<<.....<<..>>....<<<<<<<<<....
>>>>>>>>>....>>......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7afo A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
• Resolution: 3.93 Å
• Binding residue (original residue number in PDB): Q17 P115 Y116 N117 Q141 E143 R147 K155 K186 V187 N219 R221 R222 K223 T224 R226 N227 R248
• Binding residue (residue number reindexed from 1): Q1 P99 Y100 N101 Q125 E127 R131 K139 K170 V171 N203 R205 R206 K207 T208 R210 N211 R232

Enzymatic activity

• Enzyme Commision number: 2.1.1.182: 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase.

Gene Ontology

Molecular Function

• GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity
• GO:0003690 double-stranded DNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0008168 methyltransferase activity
• GO:0016433 rRNA (adenine) methyltransferase activity
• GO:0043024 ribosomal small subunit binding
• GO:0052908 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000154 rRNA modification
• GO:0006364 rRNA processing
• GO:0030490 maturation of SSU-rRNA
• GO:0031167 rRNA methylation
• GO:0032259 methylation
• GO:0046677 response to antibiotic
• GO:0070475 rRNA base methylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:7afo, PDBe:7afo, PDBj:7afo
• PDBsum: 7afo
• PubMed: 34088665
• UniProt: P06992|RSMA_ECOLI Ribosomal RNA small subunit methyltransferase A (Gene Name=rsmA)