Structure of PDB 7nac Chain w Binding Site BS01

Receptor Information

>7nac Chain w (length=672) Species: 1247190 (Saccharomyces cerevisiae BY4741)

MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVV
IDLCAAPGSWCQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDC
RSKLRGYMKTWKADTVLHDGAPNVGLGWVQDAFTQSQLTLQALKLAVENL
VVNGTFVTKIFRSKDYNKLIWVFQQLFEKVEATKPPASRNVSAEIFVVCK
GFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKVRKRQGYEEGD
NLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEF
RSCIEDLKVLGKKDFKMILRWRKIAREILTEEEQIEKDLQGLQEKQRLNV
KRERRRKNEMKQKELQRMQMNMESLFNLKTAEKTGILNDLAKGKKRMIFT
MIKDKDSAADADDLESELNAMYSDYKTRRSERDAKFRAKQARGGDNEEEW
TGFAITNLISKLKGQEGDHKLSSKARMIFNDPIFNNVEPSDFEIVANDFD
SDYDSEEEKNQTKKEKHSRDIDIATVEAMTLAHQLALGQKNKHDLVDEGF
NRYTFRDTENLPDWFLEDEKEHSKINKPITKEAAMAIKEKIKAMNARPIK
KVAEAKARKRMRAVARLEKIKKKAGLVTLVVASGRNKGLAGRPKGVKGKY
KMVDGVMKNEQRALRRIAKKHH

Ligand information

>7nac Chain 1 (length=2661)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaagu
acagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacg
ugaaauuguugaaagggaagggcauuugaucagacaugguguuuugugcc
cucugcuccuuguggguaggggaaucucgcauuucacugggccagcauca
guuuugguggcaggauaaauccauaggaauguagcuugccucgguaagua
uuauagccugugggaauacugccagcugggacugaggacugcgacguaag
ucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggac
caaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgu
aaugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccg
auccugaggauggauuugaguaagagcauagcuguugggacccgaaagau
ggugaacuaugccugaauagggugaagccagaggaaacucugguggaggc
ucggcggucgaucgucgaauuuggguauaggggcgaaagacaaccaucua
guagcugguuccugccgaaguuucccucaggauagcagaagcucguauca
guuuuaugaauguaagaaugaagagcuuuuagugggccauuuuugguaag
cagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccggaau
acacgcucaucagacaccacaaaagguguuaguucaucuagacagccgga
cgguggccauggaagucggaauccgcuaaggaguguguaacaacucaccg
gccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccuau
acucuaccgucaggguugauaugaugcccugacgaguaggcaggcgugga
ggucagugacgaagccuagaccguaaggucgggucgaacggccucuagug
cagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacuga
aguggggaaagguuccacgucaacagcaguuggacguggguuagucgauc
cuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggccac
caucgaaagggaauccgguuaagauuccggaaccuggauauggauucuuc
acgguaacguaacugaauguggagacgucggcgcgagcccugggaggagu
uaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccggaga
uggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgc
uugugacggcccgugaaaauccacaggaaggaauaguuuucaugccaggu
cguacuucuccaaggugaacagccucuaguugauagaauaauguagauaa
gggaagucgguccguaacuucgggauaaggauuggcucuaagggucgggu
agugagggccuuggucacggccuuggcuugcuacaauuaacgaucaacuu
agaacugguacggacaaggggaaucugacuguuaacgagauucccacugu
cccuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaga
aucagcggggaacccuguugagcuugacucuaguuugacauugugaagag
acauagaggguguagaauaagugggagcuucggcgccagugaaauaccac
uaccuuuauaguuucuuuacuauugucagguggggaguaaaguuaccaca
gggauaacuggcuuguggcagucaagcguucauagcgacauugcucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugaauguuaccgcaauaguaauugaacuuaguacgagag
gaacaguucauucggauaauugguuuuugcggcugucugaucaggcauug
ccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucagaa
uccaugcuagaacgcggugauuucuuugcuccacacaauauagauggaua
cgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacgg
ugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucau
uuugcguggggauaaaucauuuguauacgacuuagauguacaacggggua
uuguaagcaguagaguagccguuacgaucugcugagauuaagccuuuguu
gucugauuugu

..........................<<<<<<.....<<....>>.....
.>>>>>.>.........<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<..<<.......<<.<<<<<<...>>>>>>.>>......
.>>....<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......
>>>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<<..>>>>>>..>>>.................................
.<<....>>...............<<<<....>>>>..............
....................<<<<<.<<<<<.....<<<<<....<<..<
<<<<<<<<.....>>>>>>>>>......>>....>>>>>.<<<<<<<.<<
<<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>.
......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>
>>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<
<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>..
.<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<.<
<<<<.......>>>.>>..>>....>>>>>>.>>>>>>..<<.<...<<<
<<<...<<<<<<<<<<...<<<....<<<<<<<....>>>>>>>.....>
>>.<<<<....>>>>.....>>>>>>>>>>...<....>...>>>>>>..
....>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<...<<<
.<<<<<<....>>>>.>>>>>.>>>>>>>>.>>..<<<<.<<<<<.....
>>>>>.>>>>....<<<......>>>...<<<<<<<..<<<<(((.....
<<<<<<.....<<..........<<<.<<<<<<<<<<.......<<<<<.
<<....<<.........>>....>>.........<<......>>...>>>
>>...>>>>>>>>>>>>>..........))).>>...>>>>>>.>>>>..
>>>>>>><<<<<<<<<.........>>>>>>>>>....>>>>>>..<<<<
<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>...
.....>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<..
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<
<...<<....<<<....>>>........<<<<<<........>>>>>>..
..>>....>>...<<<<<........>>>>>))<<<<.<<<<<<......
<<<....>>>.......<<<<<<...<<<<.<<<<<<<.<<<<<<<<<<.
.(((..>>>>>><...<<<<<....<<<<<<....<<<.....>>>....
>>>>>>.....>>>>>....><<<<<<<......>>>>>>>>>>>...>>
>>>>>.>>>>.........>>>>>>............>>.>>>>>>>>>>
>>..>>>>>>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.
<<........<<<<<<.<<<<.....................<<<<<.<<
<<<<<<..<<..<<<<..>>>>..>>>>>>>>>>......>>>>>.....
.>>>...>>>>>>>....<<<<<<<<<........>>.>>>>>>>.....
>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>....
<<<<<..<<<..<<<<<<.<<<<<<..<<<<.<<<<.<<...<<<<<<<<
<<..<<<.<..........<<<<<..<<<..>>>............>>>>
>..>>>>...>>>>>>>>>>....>>.>>>>..>>>>..>>>>>.>.>>>
>>>.............<<<<<<...<<.......>>...>>>>>>.....
..<<<<..<.<<<<<<<......>>>>>>>...>.<<<.........>>>
.....>>>>.................<<<<<<<....>>>.>>>>.....
...>>>.>>>>>....<<<<<<<<..<<<<.<.<<<<<<...........
....>>>>>>.><<<<<...<<<<....<<<<<<<<<<))).>>>>>..>
>>>>...>>>>..>>>>>.<<<<...<<<<<...........>>>>>...
>>>>.>>>>....>>>>>>>>.......<<<<<<.<<<.<<....<<...
.......<<<<<<.....>>>>>>......>>.......<<<<<<...<<
<<<.<..<<<......>>>..>.>>>>>.>>>>>>.............>>
.>>>.>>>>>>..<<<<<.<.............>.....<<<<<<<<<.<
<<....<<<<....<<.......>>...>>>>...>>>....>>>>.>>>
>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7nac Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
• Resolution: 3.04 Å
• Binding residue (original residue number in PDB): M1 G2 K3 T4 Q5 K6 K7 N8 S9 K10 R12 Y17 A27 R28 P122 N123 V124 G125 K159 R162 S163 T183 K184 R189 N190 S192 A193 E194 R241 R243 R369 R372 R384 K451 Y473 R686 I709 N710 A730 R731 A739 R742 K743 R744 R746 R750 L751 G800 V819 D820 G821 V822 K824 N825 R828 R832 H837
• Binding residue (residue number reindexed from 1): M1 G2 K3 T4 Q5 K6 K7 N8 S9 K10 R12 Y17 A27 R28 P122 N123 V124 G125 K159 R162 S163 T183 K184 R189 N190 S192 A193 E194 R241 R243 R352 R355 R367 K403 Y425 R552 I575 N576 A596 R597 A605 R608 K609 R610 R612 R616 L617 G634 V653 D654 G655 V656 K658 N659 R662 R666 H671

Enzymatic activity

• Enzyme Commision number: 2.1.1.167: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase.

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008168 methyltransferase activity
• GO:0008649 rRNA methyltransferase activity
• GO:0008650 rRNA (uridine-2'-O-)-methyltransferase activity
• GO:0016435 rRNA (guanine) methyltransferase activity
• GO:0070039 rRNA (guanosine-2'-O-)-methyltransferase activity

Biological Process

• GO:0000451 rRNA 2'-O-methylation
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0001510 RNA methylation
• GO:0006364 rRNA processing
• GO:0031167 rRNA methylation
• GO:0032259 methylation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:7nac, PDBe:7nac, PDBj:7nac
• PDBsum: 7nac
• PubMed: 36482249
• UniProt: P25582|SPB1_YEAST 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase (Gene Name=SPB1)