Q12460

PR
Gene name
NOP56 (SIK1, YLR197W, L8167.9)
Protein name
Nucleolar protein 56
Names
Ribosome biosynthesis protein SIK1, Suppressor of I kappa b protein 1
Species
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
KEGG Pathway
sce:YLR197W
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

407-504 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

26 structures for Q12460

Entry ID Method Resolution Chain Position Source
5WLC EM 380 A SA 1-504 PDB
5WYJ EM 870 A 3D 1-504 PDB
5WYK EM 450 A 3D 1-504 PDB
6KE6 EM 340 A 3D 1-504 PDB
6LQP EM 320 A 3D 1-504 PDB
6LQQ EM 410 A 3D 1-504 PDB
6LQR EM 860 A 3D 1-504 PDB
6LQS EM 380 A 3D 1-504 PDB
6LQT EM 490 A 3D 1-504 PDB
6LQU EM 370 A 3D 1-504 PDB
6LQV EM 480 A 3D 1-504 PDB
6ND4 EM 430 A a 1-504 PDB
6ZDT X-ray 171 A B 1-166 PDB
6ZQA EM 440 A CD 1-504 PDB
6ZQB EM 390 A CD 1-504 PDB
6ZQC EM 380 A CD 1-504 PDB
6ZQD EM 380 A CD 1-504 PDB
6ZQE EM 710 A CD 1-504 PDB
7AJT EM 460 A CD 1-504 PDB
7AJU EM 380 A CD 1-504 PDB
7D4I EM 400 A 3D 1-504 PDB
7D5S EM 460 A 3D 1-504 PDB
7D5T EM 600 A 3D 1-504 PDB
7D63 EM 1230 A 3D 1-504 PDB
7SUK EM 399 A SA 3-415 PDB
AF-Q12460-F1 Predicted AlphaFoldDB

3 variants for Q12460

Variant ID(s) Position Change Description Diseaes Association Provenance
s12-546357 87 P>S No SGRP
s12-546384 96 I>V No SGRP
s12-547495 466 K>R No SGRP

No associated diseases with Q12460

3 regional properties for Q12460

Type Name Position InterPro Accession
domain Nop domain 180 - 417 IPR002687
domain Nucleolar protein 58/56, N-terminal 6 - 72 IPR012974
domain NOSIC 173 - 225 IPR012976

Functions

Description
EC Number
Subcellular Localization
  • Nucleus, nucleolus
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

6 GO annotations of cellular component

Name Definition
90S preribosome A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
box C/D RNP complex A ribonucleoprotein complex containing a box C/D type RNA that can carry out ribose-2'-O-methylation of target RNAs. Box C/D type RNAs are widespread in eukaryotes and in Archaea, suggesting that an RNA-based guide mechanism for directing specific RNA 2'-O-ribose methylations was present in the common ancestor of Archaea and Eukarya.
nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
small-subunit processome A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.

2 GO annotations of molecular function

Name Definition
mRNA binding Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
snoRNA binding Binding to a small nucleolar RNA.

5 GO annotations of biological process

Name Definition
box C/D RNA 3'-end processing Any process involved in forming the mature 3' end of a box C/D RNA molecule.
maturation of SSU-rRNA Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule.
rRNA modification The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
rRNA processing Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
snoRNA guided rRNA 2'-O-methylation The posttranscriptional addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of methylation.

2 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
O00567 NOP56 Nucleolar protein 56 Homo sapiens (Human) PR
Q9D6Z1 Nop56 Nucleolar protein 56 Mus musculus (Mouse) PR
10 20 30 40 50 60
MAPIEYLLFE EPTGYAVFKV KLQQDDIGSR LKEVQEQIND FGAFTKLIEL VSFAPFKGAA
70 80 90 100 110 120
EALENANDIS EGLVSESLKA ILDLNLPKAS SKKKNITLAI SDKNLGPSIK EEFPYVDCIS
130 140 150 160 170 180
NELAQDLIRG VRLHGEKLFK GLQSGDLERA QLGLGHAYSR AKVKFSVQKN DNHIIQAIAL
190 200 210 220 230 240
LDQLDKDINT FAMRVKEWYG WHFPELAKLV PDNYTFAKLV LFIKDKASLN DDSLHDLAAL
250 260 270 280 290 300
LNEDSGIAQR VIDNARISMG QDISETDMEN VCVFAQRVAS LADYRRQLYD YLCEKMHTVA
310 320 330 340 350 360
PNLSELIGEV IGARLISHAG SLTNLSKQAA STVQILGAEK ALFRALKTKG NTPKYGLIYH
370 380 390 400 410 420
SGFISKASAK NKGRISRYLA NKCSMASRID NYSEEPSNVF GSVLKKQVEQ RLEFYNTGKP
430 440 450 460 470 480
TLKNELAIQE AMELYNKDKP AAEVEETKEK ESSKKRKLED DDEEKKEKKE KKSKKEKKEK
490 500
KEKKDKKEKK DKKEKKDKKK KSKD