Structure of PDB 6by1 Chain DC Binding Site BS01

Receptor Information

>6by1 Chain DC (length=271) Species: 83333 (Escherichia coli K-12)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>6by1 Chain DA (length=2869)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuuggcuuugaaguguggacgccagucugcauggagccgaaaauaca
uguuugauguucuaacguugacccguaauccggguugcggacagugucug
guggguaguuugacuggggcggucuccuccuaaagaguaacggaggagca
cgaagguuggcuaauccuggucggacaucaggagguuagugcaauggcau
aagccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcaggu
cauagugauccggugguucugaauggaagggccaucgcucaacggauaaa
agguacuccggggauaacaggcugauaccgcccaagaguucauaucgacg
gcgguguuuggcaccucgaugucggcucaucacauccuggggcugaagua
ggucccaaggguauggcuguucgccauuuaaagugguacgcgagcugggu
uuagaacgucgugagacaguucggucccuaucugccgugggcgcuggaga
acugaggggggcugcuccuaguacgagaggaccggaguggacgcaucacu
gguguucggguugucaugccaauggcacugcccgguagcuaaaugcggaa
gagauaagugcugaaagcaucuaagcacgaaacuugccccgagaugaguu
cucccugacccuuuaaggguccugaaggaacguugaagacgacgacguug
auaggccggguguguaagcgcagcgaugcguugagcuaaccgguacuaau
gaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<........<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>.>....>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<<<..>>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.<<<<.....>>>>..>>..
.>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<..<<<<<..<<........
<<<<<.<<...<<<.........>>>...>>........<<<......>>
>..>>>>>....>>..>>>>>.>>...........))).....>>>>>>.
>>>...>>>>>>><<<<<<<<<....>>>>>>>>>....>>>>>><<<<<
<<...<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.>>
.....>>>>>><......<<.....<<<<<<.......>>>>>><<<<..
..<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<
<...<<<...<<<....>>>...>>>...>>>..<<<<<........>>>
>>))<<<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<
....(((...>>>>>><<..<<<<...<<<.<<<<<<<<.<.......>>
>>>>>>>...>>>...>>>>...>><..<<<<<....>>>>>...>>>>>
>...>>>...>>>>.........>>>>...>>....>>>>>>>>>>>.>>
>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<
<....<<<<<<<<.<<...............<<<<<....<<..>>....
.>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
...<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<
<<.......<<<.<..<<....>>...>.>>>.......>>>>>>>>>..
>>>>><<<<<<.......>>>>>>........<...........<<<<<<
.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>
>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<
.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<
<<....<<<......<<<<<<<<....>>>>>>>>...>>>.........
..>>>>>>>>>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>
>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>..
..>>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>
))).......<<<<<<<.((..>>>>..))>>>>>>>.............
>>>>..]]>>>>.......<<<<.<.<<<<<<...<<.......>>...>
>>>>>...>>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......
>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>.
...<<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....<<<<<
<<...<<<<..<<<<<<<...............>>>>>>>.<<<<<...<
<<<...<<<<<<<<<<<))).>>>>>>..>>>>>...>>>>.>>>>>...
<<<....<<<<<...........>>>>>....>>>.>>>>.......>>>
>>>>..<<<<<.....>>>>><....<<..<<<<<.......>>>>>...
.<<<<<<<<..<<....<<<<<....>>>>>...>>...>>>>>.>>>..
...>>..>..>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6by1 Structural evidence for product stabilization by the ribosomal mRNA helicase.
• Resolution: 3.94 Å
• Binding residue (original residue number in PDB): K6 P7 T8 S9 P10 G11 R12 R13 H14 K25 E34 K35 N36 K38 S39 G41 R42 N43 N44 N45 G46 R47 I48 T49 T50 R51 H52 I53 G55 H57 K58 A60 Y61 R62 I73 Y82 P84 R86 D97 G98 E99 R100 M145 K146 K149 L153 A154 R155 S156 A157 G158 T159 Y170 L175 S177 E179 R181 E184 A197 H199 M200 V203 L204 G205 K206 A207 G208 R211 W212 R213 R216 P217 T218 V219 R220 G221 M224 N225 P226 D228 H229 H231 G233 E235 G236 R237 N238 F239 G240 K241 H242 P243 P246 W247 T251 K252 G253 K254 K255 T256 R257 S258 N259 K260 R261 T262 R269 R270
• Binding residue (residue number reindexed from 1): K6 P7 T8 S9 P10 G11 R12 R13 H14 K25 E34 K35 N36 K38 S39 G41 R42 N43 N44 N45 G46 R47 I48 T49 T50 R51 H52 I53 G55 H57 K58 A60 Y61 R62 I73 Y82 P84 R86 D97 G98 E99 R100 M145 K146 K149 L153 A154 R155 S156 A157 G158 T159 Y170 L175 S177 E179 R181 E184 A197 H199 M200 V203 L204 G205 K206 A207 G208 R211 W212 R213 R216 P217 T218 V219 R220 G221 M224 N225 P226 D228 H229 H231 G233 E235 G236 R237 N238 F239 G240 K241 H242 P243 P246 W247 T251 K252 G253 K254 K255 T256 R257 S258 N259 K260 R261 T262 R269 R270

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0032297 negative regulation of DNA-templated DNA replication initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990082 DnaA-L2 complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6by1, PDBe:6by1, PDBj:6by1
• PDBsum: 6by1
• PubMed: 30552154
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)