P32684 (RLUF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribosomal large subunit pseudouridine synthase F
EC=5.4.99.21

Alternative name(s):
23S rRNA pseudouridine(2604) synthase
rRNA pseudouridylate synthase F
rRNA-uridine isomerase F

Gene names

Name:	rluF
Synonyms:	yjbC
Ordered Locus Names:	b4022, JW3982

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	290 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Responsible for synthesis of pseudouridine from uracil-2604 in 23S ribosomal RNA. Can, to a small extent, also react with uracil-2605. Ref.4
Catalytic activity	23S rRNA uridine(2604) = 23S rRNA pseudouridine(2604). Ref.4 Ref.6
Subunit structure	Monomer. Ref.5
Sequence similarities	Belongs to the pseudouridine synthase RsuA family. Contains 1 S4 RNA-binding domain.

Ontologies

Keywords
Biological process	rRNA processing
Ligand	RNA-binding
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	enzyme-directed rRNA pseudouridine synthesis Inferred from mutant phenotype Ref.4. Source: EcoCyc
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW pseudouridine synthase activity Inferred from mutant phenotype Ref.4. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 290

290

Ribosomal large subunit pseudouridine synthase F

PRO_0000100016

Regions

Domain

7 – 72

66

S4 RNA-binding

Region

105 – 108

4

Interaction with RNA

Region

187 – 190

4

Interaction with RNA

Sites

Active site

107

1

Nucleophile Probable

Experimental info

Mutagenesis

107

1

D → N or T: Loss of activity. Ref.4

Secondary structure

1

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290

Helix Strand Turn

Details...

Helix

9 – 14

6

Turn

15 – 17

3

Helix

21 – 29

9

Beta strand

33 – 35

3

Beta strand

52 – 54

3

Beta strand

57 – 59

3

Helix

64 – 66

3

Beta strand

69 – 74

6

Beta strand

82 – 85

4

Beta strand

87 – 89

3

Helix

90 – 93

4

Beta strand

101 – 104

4

Beta strand

111 – 118

8

Helix

120 – 132

13

Beta strand

135 – 143

9

Helix

147 – 153

7

Beta strand

160 – 163

4

Beta strand

168 – 173

6

Beta strand

176 – 181

6

Helix

188 – 195

8

Beta strand

200 – 208

9

Beta strand

221 – 223

3

Helix

226 – 233

8

Sequences

	Sequence		Length	Mass (Da)
	P32684 [UniParc]. Last modified October 1, 1993. Version 1. Checksum: C88C830CBE5DF2FA	FASTA	290	32,477
	10 20 30 40 50 60 MLPDSSVRLN KYISESGICS RREADRYIEQ GNVFLNGKRA TIGDQVKPGD VVKVNGQLIE 70 80 90 100 110 120 PREAEDLVLI ALNKPVGIVS TTEDGERDNI VDFVNHSKRV FPIGRLDKDS QGLIFLTNHG 130 140 150 160 170 180 DLVNKILRAG NDHEKEYLVT VDKPITEEFI RGMSAGVPIL GTVTKKCKVK KEAPFVFRIT 190 200 210 220 230 240 LVQGLNRQIR RMCEHFGYEV KKLERTRIMN VSLSGIPLGE WRDLTDDELI DLFKLIENSS 250 260 270 280 290 SEVKPKAKAK PKTAGIKRPV VKMEKTAEKG GRPASNGKRF TSPGRKKKGR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli." Del Campo M., Kaya Y., Ofengand J. RNA 7:1603-1615(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-107. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA." Sunita S., Zhenxing H., Swaathi J., Cygler M., Matte A., Sivaraman J. J. Mol. Biol. 359:998-1009(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 66-290, PARTIAL PROTEIN SEQUENCE, SUBUNIT, MASS SPECTROMETRY.
[6]	"Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome." Alian A., DeGiovanni A., Griner S.L., Finer-Moore J.S., Stroud R.M. J. Mol. Biol. 388:785-800(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE RNA, CATALYTIC ACTIVITY, ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00006 Genomic DNA. Translation: AAC43116.1.
U00096 Genomic DNA. Translation: AAC76992.1.
AP009048 Genomic DNA. Translation: BAE78024.1.

PIR

E65209.

RefSeq

NP_418446.1. NC_000913.2.
YP_492165.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2GML	X-ray	2.60	A/B	66-290	[»]
3DH3	X-ray	3.00	A/B/C/D	1-290	[»]

ProteinModelPortal

P32684.

SMR

P32684. Positions 3-243.

ModBase

Search...

Protein-protein interaction databases

IntAct

P32684. 9 interactions.

STRING

511145.b4022.

Proteomic databases

PaxDb

P32684.

PRIDE

P32684.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76992; AAC76992; b4022.
BAE78024; BAE78024; BAE78024.

GeneID

12932783.
948519.

KEGG

ecj:Y75_p3909.
eco:b4022.

PATRIC

32123573. VBIEscCol129921_4135.

Organism-specific databases

EchoBASE

EB1865.

EcoGene

EG11921. rluF.

Phylogenomic databases

eggNOG

COG1187.

HOGENOM

HOG000044954.

KO

K06182.

OMA

MNVSLKG.

ProtClustDB

PRK10475.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11921-MONOMER.
ECOL316407:JW3982-MONOMER.
MetaCyc:EG11921-MONOMER.

Gene expression databases

Genevestigator

P32684.

Family and domain databases

Gene3D

3.10.290.10. 1 hit.

InterPro

IPR020103. PsdUridine_synth_cat_dom.
IPR000748. PsdUridine_synth_RsuA/RluB/E/F.
IPR018496. PsdUridine_synth_RsuA/RluB_CS.
IPR006145. PsdUridine_synth_RsuA/RluD.
IPR002942. S4_RNA-bd.
[Graphical view]

Pfam

PF00849. PseudoU_synth_2. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]

SMART

SM00363. S4. 1 hit.
[Graphical view]

SUPFAM

SSF55120. PsdUridine_synth_cat_dom. 1 hit.

TIGRFAMs

TIGR00093. TIGR00093. 1 hit.

PROSITE

PS01149. PSI_RSU. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P32684.

Entry information

Entry name

RLUF_ECOLI

Accession

Primary (citable) accession number: P32684
Secondary accession number(s): Q2M6T2

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1993
Last modified:	May 1, 2013
This is version 106 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program