Structure of PDB 7naf Chain w

Receptor sequence

>7nafw (length=361) Species: 1247190 (Saccharomyces cerevisiae BY4741)

MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVV
IDLCAAPGSWCQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDC
RSKLRGYMKTWKADTVLHDGAPNVGLGWVQDAFTQSQLTLQALKLAVENL
VVNGTFVTKIFRSKDYNKLIWVFQQLFEKVEATKPPASRNVSAEIFVVCK
GFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKVRKRQGYEEGD
NLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEF
RSCIEDLKVLGKKDFKMILRWRKIAREILGLQEKQRLNVKRERRRKNEMK
QKELQRMQMNM

3D structure

• PDB: 7naf Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
• Chain: w
• Resolution: 3.13 Å

Enzymatic activity

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

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	w	M1 G2 K3 T4 K6 K7 S9 R12 Y17 K21 A27 R28 S29 K32 A121 P122 N123 V124 G125 W128 K159 F161 R162 S163 T183 K184 R189 N190 V191 S192 A193 E194 V240 R241 R243 K368 R372 R373 R384	M1 G2 K3 T4 K6 K7 S9 R12 Y17 K21 A27 R28 S29 K32 A121 P122 N123 V124 G125 W128 K159 F161 R162 S163 T183 K184 R189 N190 V191 S192 A193 E194 V240 R241 R243 K340 R344 R345 R356
BS02	peptide	w	V70 N71	V70 N71
BS03	SAH	w	S29 C54 A55 A56 S59 I79 D119 L138	S29 C54 A55 A56 S59 I79 D119 L138

Gene Ontology

Molecular Function

• GO:0008168 methyltransferase activity

Biological Process

• GO:0001510 RNA methylation
• GO:0032259 methylation

External links

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