Structure of PDB 4v95 Chain AY Binding Site BS01

Receptor Information

>4v95 Chain AY (length=132) Species: 83333 (Escherichia coli K-12)

IVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEY
YKERLLAASHHLISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTE
KKARRPTRPTRASKERRLASKAQKSSVKAMRG

Ligand information

>4v95 Chain AA (length=1466)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggccguggucagcggcggacgggugagua
acgcgugggugaccuacccggaagagggggacaacccggggaaacucggg
cuaaucccccauguggacccgccccuugggguguguccaaagggcuuugc
ccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaauggc
ccaccaaggcgacgacggguagccggucugagaggauggccggccacagg
ggcacugagacacgggccccacuccuacgggaggcagcaguuaggaaucu
uccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagc
ccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggga
cugacgguaccgggguaauagcgccggccaacuccgugccagcagccgcg
guaauacggagggcgcgagcguuacccggauucacugggcguaaagggcg
uguaggcggccuggggcgucccaugugaaagaccacggcucaaccguggg
ggagcgugggauacgcucaggcuagacggugggagagggugguggaauuc
ccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaa
ggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggagc
aaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuag
gucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccug
gggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgca
caagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuacc
aggccuugacaugcccgggugaaagccugggcacaggugcugcauggccg
ucgucagcucgugccgugagguguuggguuaagucccgcaacgagcgcaa
cccccgccguuaguugccagcgguucggccgggcacucuaacgggacugc
ccgcgaaagcgggaggaaggaggggacgacgucuggucagcauggcccuu
acggccugggcgacacacgugcuacaaugcccacuacaaagcgaugccac
ccggcaacggggagcuaaucgcaaaaaggugggcccaguucggauugggg
ucugcaacccgaccccaugaagccggaaucgcuaguaaucgcggaucagc
caugccgcggugaauacguucccgggccuuguacacaccgcccgucacgc
caugggagcgggcucuacccgaagucgccgggagccuacgggcaggcgcc
gaggguagggcccgugacuggggcgaagucguaacaagguagcuguaccg
gaaggugcggcuggau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v95 Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): T108 P110 S114 R117 R118 L119 K122 A123 Q124 M131 R132
• Binding residue (residue number reindexed from 1): T107 P109 S113 R116 R117 L118 K121 A122 Q123 M130 R131

Enzymatic activity

• Enzyme Commision number: 3.1.1.29: peptidyl-tRNA hydrolase.

Gene Ontology

Molecular Function

• GO:0003747 translation release factor activity
• GO:0004045 aminoacyl-tRNA hydrolase activity
• GO:0016787 hydrolase activity
• GO:0043022 ribosome binding

Biological Process

• GO:0006415 translational termination
• GO:0006417 regulation of translation
• GO:0072344 rescue of stalled ribosome

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4v95, PDBe:4v95, PDBj:4v95
• PDBsum: 4v95
• PubMed: 22422986
• UniProt: P40711|ARFB_ECOLI Peptidyl-tRNA hydrolase ArfB (Gene Name=arfB)