P0CH07 (RL402_SCHPO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-60S ribosomal protein L40

Cleaved into the following 2 chains:

1. Ubiquitin
2. 60S ribosomal protein L40
   Alternative name(s):
   CEP52

Gene names

Name:	ubi2
Synonyms:	uep1
ORF Names:	SPAC1805.12c

Organism

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) [Reference proteome]

Taxonomic identifier

284812 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › Taphrinomycotina › Schizosaccharomycetes › Schizosaccharomycetales › Schizosaccharomycetaceae › Schizosaccharomyces › Schizosaccharomyces pombe

Protein attributes

Sequence length	128 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity. Ribosomal protein L40 is a component of the 60S subunit of the ribosome.
Subunit structure	Ribosomal protein L40 is part of the 60S ribosomal subunit By similarity.
Subcellular location	Ubiquitin: Cytoplasm By similarity. Nucleus By similarity. 60S ribosomal protein L40: Cytoplasm By similarity.
Miscellaneous	Ubiquitin is encoded by 5 different genes. Ubi1 and ubi2 are synthesized as a polyprotein with one copy of ubiquitin fused to ribosomal protein L40. Ubi3 and ubi5 are polyproteins with one copy of ubiquitin fused to ribosomal proteins S27a and s27b respectively. Ubi4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.
Sequence similarities	In the N-terminal section; belongs to the ubiquitin family. In the C-terminal section; belongs to the ribosomal protein L40e family. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Cytoplasm Nucleus
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW cytoplasmic translation Non-traceable author statement. Source: PomBase ribosome biogenesis Inferred from sequence orthology. Source: PomBase
Cellular_component	cytosolic large ribosomal subunit Inferred from sequence orthology. Source: PomBase nucleolus Inferred from direct assay PubMed 16823372. Source: PomBase
Molecular_function	structural constituent of ribosome Inferred from sequence orthology. Source: PomBase
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 76

76

Ubiquitin

PRO_0000396452

Chain

77 – 128

52

60S ribosomal protein L40

PRO_0000396453

Regions

Domain

1 – 76

76

Ubiquitin-like

Amino acid modifications

Cross-link

6

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Cross-link

11

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Cross-link

27

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Cross-link

29

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

33

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Cross-link

48

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

63

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

76

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

128

Helix Strand Turn

Details...

Beta strand

1 – 7

7

Beta strand

12 – 18

7

Helix

23 – 34

12

Helix

38 – 40

3

Beta strand

42 – 45

4

Helix

56 – 59

4

Beta strand

66 – 70

5

Sequences

	Sequence		Length	Mass (Da)
	P0CH07 [UniParc]. Last modified August 10, 2010. Version 1. Checksum: A35EA817EFD46D38	FASTA	128	14,595
	10 20 30 40 50 60 MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 70 80 90 100 110 120 IQKESTLHLV LRLRGGIIEP SLKALASKYN CEKQICRKCY ARLPPRATNC RKKKCGHTNQ LRPKKKLK

References

[1]

"The genome sequence of Schizosaccharomyces pombe." Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M. , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P. Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 972 / ATCC 24843.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

CU329670 Genomic DNA. Translation: CAB55853.1.

PIR

T37547.

RefSeq

NP_593923.1. NM_001019352.2.
NP_594398.1. NM_001019821.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4II2	X-ray	2.20	B	1-76	[»]
4II3	X-ray	2.90	B/D	1-76	[»]

ProteinModelPortal

P0CH07.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

SPAC11G7.04.1; SPAC11G7.04.1:pep; SPAC11G7.04.
SPAC1805.12c.1; SPAC1805.12c.1:pep; SPAC1805.12c.

GeneID

2541768.
2542428.

KEGG

spo:SPAC11G7.04.
spo:SPAC1805.12c.

Organism-specific databases

PomBase

SPAC11G7.04.
SPAC1805.12c.

Phylogenomic databases

KO

K02927.

OrthoDB

EOG48WGBH.

Family and domain databases

InterPro

IPR001975. Ribosomal_L40e.
IPR000626. Ubiquitin.
IPR019954. Ubiquitin_CS.
IPR019956. Ubiquitin_subgr.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]

PRINTS

PR00348. UBIQUITIN.

SMART

SM00213. UBQ. 1 hit.
[Graphical view]

PROSITE

PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

20802859.

Entry information

Entry name

RL402_SCHPO

Accession

Primary (citable) accession number: P0CH07
Secondary accession number(s): O13697 , O14257, P0C014, P0C015, Q76PD0, Q9HDZ4

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 10, 2010
Last sequence update:	August 10, 2010
Last modified:	May 1, 2013
This is version 20 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program