Structure of PDB 7nac Chain w

Receptor sequence

>7nacw (length=672) Species: 1247190 (Saccharomyces cerevisiae BY4741) [Search protein sequence]

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

3D structure

PDB

7nac Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.

Chain

Resolution

3.04 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

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 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	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
BS02	SAH	w	S29 C54 A55 A56 S59 W60 D78 I79 D94 D119 L138	S29 C54 A55 A56 S59 W60 D78 I79 D94 D119 L138

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

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)

[Back to BioLiP]