P00654 (RNU2_USTSP) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonuclease U2
Short name=RNase U2
EC=3.1.27.4

Gene names

Name:

RNU2

Organism

Ustilago sphaerogena (Smut fungus)

Taxonomic identifier

5271 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Basidiomycota › Ustilaginomycotina › Ustilaginomycetes › Ustilaginales › Ustilaginaceae › Ustilago

Protein attributes

Sequence length	114 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in A-P or G-P with 2',3'-cyclic phosphate intermediates.
Miscellaneous	After treatment by base Asn-32 and Asp-45 partially isomerise by succinimide rearrangement to form iosaspartyl peptides.
Sequence similarities	Belongs to the ribonuclease U2 family.

Ontologies

Keywords
Ligand	Calcium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
PTM	Disulfide bond
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Molecular_function	RNA binding Inferred from electronic annotation. Source: InterPro ribonuclease U2 activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 114

114

Ribonuclease U2

PRO_0000137379

Regions

Region

39 – 49

11

Substrate binding

Region

108 – 110

3

Substrate binding

Sites

Active site

41

1

Ref.5

Active site

62

1

Proton acceptor Ref.5

Active site

101

1

Proton donor Ref.5

Metal binding

29

1

Calcium 1

Metal binding

29

1

Calcium 2

Metal binding

30

1

Calcium 1; via carbonyl oxygen

Metal binding

31

1

Calcium 2; via carbonyl oxygen

Metal binding

32

1

Calcium 1

Metal binding

32

1

Calcium 2

Metal binding

37

1

Calcium 1

Metal binding

39

1

Calcium 2; via carbonyl oxygen

Binding site

85

1

Substrate

Site

62

1

Methylation inactivates enzyme Ref.6

Amino acid modifications

Disulfide bond

1 ↔ 54

Ref.4

Disulfide bond

9 ↔ 113

Ref.4

Disulfide bond

55 ↔ 96

Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

114

Helix Strand Turn

Details...

Beta strand

5 – 9

5

Beta strand

12 – 15

4

Helix

16 – 31

16

Helix

36 – 38

3

Beta strand

41 – 43

3

Helix

47 – 49

3

Beta strand

60 – 64

5

Beta strand

75 – 77

3

Beta strand

83 – 89

7

Turn

90 – 92

3

Beta strand

95 – 101

7

Beta strand

105 – 109

5

Sequences

	Sequence		Length	Mass (Da)
	P00654 [UniParc]. Last modified December 15, 1998. Version 4. Checksum: 96D32CB2E23AAB98	FASTA	114	12,387
	10 20 30 40 50 60 CDIPQSTNCG GNVYSNDDIN TAIQGALDDV ANGDRPDNYP HQYYDEASED ITLCCGSGPW 70 80 90 100 110 SEFPLVYNGP YYSSRDNYVS PGPDRVIYQT NTGEFCATVT HTGAASYDGF TQCS

References

[1]	"The amino acid sequence of ribonuclease U2 from Ustilago sphaerogena." Sato S., Uchida T. Biochem. J. 145:353-360(1975) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE.
[2]	"Ribonuclease U2: cloning, production in Pichia pastoris and affinity chromatography purification of the active recombinant protein." Martinez-Ruiz A., Garcia-Ortega L., Kao R., Onaderra M., Mancheno J.M., Davies J., Martinez del Pozo A., Gavilanes J.G. FEMS Microbiol. Lett. 189:165-169(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 15-106. Strain: ATCC 12421 / CBS 534.71 / IMI 61828 / 50-135.
[3]	"Revised sequence of ribonuclease U2 in the substrate-binding region." Kanaya S., Uchida T. J. Biochem. 118:681-682(1995) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 44-53, SEQUENCE REVISION.
[4]	"The disulfide bridges of ribonuclease U2 from Ustilago sphaerogena." Sato S., Uchida T. J. Biochem. 77:1171-1176(1975) [PubMed] [Europe PMC] [Abstract] Cited for: DISULFIDE BONDS.
[5]	Uchida T., Sato S. (In) Zelinka J., Balan J. (eds.); Ribosomes and RNA metabolism, pp.453-472, Publ. House Slovak Acad. Sci., Bratislava (1973) Cited for: ACTIVE SITE.
[6]	"Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8-A resolution." Noguchi S., Satow Y., Uchida T., Sasaki C., Matsuzaki T. Biochemistry 34:15583-15591(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SEQUENCE REVISION.
[7]	"Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate." Noguchi S. Acta Crystallogr. D 66:843-849(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (0.96 ANGSTROMS) IN COMPLEX WITH CALCIUM IONS AND ADENOSINE 3'-MONOPHOSPHATE, FORMATION OF ISOASPARTATE, DISULFIDE BONDS.
[8]	"Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B." Noguchi S. Biopolymers 93:1003-1010(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.32 ANGSTROMS).
[9]	"Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca ion and 2'-adenylic acid at 1.03 A resolution." Noguchi S. Protein Pept. Lett. 17:1559-1561(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.03 ANGSTROMS) IN COMPLEX WITH CALCIUM AND ADENOSINE 2'-PHOSPHATE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ004827 Genomic DNA. Translation: CAC04098.1.

PIR

NRUSU2. PC4081.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RTU	X-ray	1.80	A	1-114	[»]
3AGN	X-ray	0.96	A	1-114	[»]
3AGO	X-ray	0.99	A	1-114	[»]
3AHS	X-ray	1.32	A/B/C	1-114	[»]
3AHW	X-ray	1.03	A	1-114	[»]

ProteinModelPortal

P00654.

SMR

P00654. Positions 1-114.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BRENDA

3.1.27.4. 6588.

Family and domain databases

Gene3D

3.10.450.30. 1 hit.

InterPro

IPR000026. Gua-sp_ribonuclease_N1/T1.
IPR016191. Ribonuclease/ribotoxin.
[Graphical view]

Pfam

PF00545. Ribonuclease. 1 hit.
[Graphical view]

SUPFAM

SSF53933. Ribonuclease/ribotoxin. 1 hit.

ProtoNet

Search...

Other

DrugBank

DB00128. L-Aspartic Acid.

EvolutionaryTrace

P00654.

Entry information

Entry name

RNU2_USTSP

Accession

Primary (citable) accession number: P00654
Secondary accession number(s): Q9HGK7

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	December 15, 1998
Last modified:	May 29, 2013
This is version 79 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program