Ribosomal large subunit pseudouridine synthase D

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Reviewed, UniProtKB/Swiss-Prot P33643 (RLUD_ECOLI)

Last modified June 16, 2009. Version 86. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Ribosomal large subunit pseudouridine synthase D
    EC=5.4.99.-
Alternative name(s):
    rRNA-uridine isomerase D
    rRNA pseudouridylate synthase D

Gene names

Name:	rluD
Synonyms:	sfhB, yfiI
Ordered Locus Names:	b2594, JW2576

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	326 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA. Ref.7
Catalytic activity	rRNA uridine = rRNA pseudouridine.
Sequence similarities	Belongs to the pseudouridine synthase rluA family. Contains 1 S4 RNA-binding domain.
Sequence caution	The sequence X57620 differs from that shown. Reason: Frameshift at position 134.

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Ontologies

Keywords
Biological process	rRNA processing
Ligand	RNA-binding
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	pseudouridine synthesis Inferred from electronic annotation. Source: InterPro rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct pseudouridine synthase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
pepQ	P21165	1	EBI-558026,EBI-552580
ycdF	P56614	1	EBI-558026,EBI-558037	From a different organism.
ydiA	P0A8A4	1	EBI-558026,EBI-548302

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed

Chain

2 – 326

325

Ribosomal large subunit pseudouridine synthase D

PRO_0000162688

Regions

Domain

18 – 91

S4 RNA-binding

Sites

Active site

139

Experimental info

Mutagenesis

139

D → N or T: Loss of activity. Ref.8

Sequence conflict

271 – 326

LRKFD…EVDWL → AGVSLTARRYMQPCCVFITR SPASKWNGMRLFHKIWWS Ref.2

Secondary structure

326

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P33643-1 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 39672B8BB559D14C
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FASTA

326

37,122

        10         20         30         40         50         60 
MAQRVQLTAT VSENQLGQRL DQALAEMFPD YSRSRIKEWI LDQRVLVNGK VCDKPKEKVL 

        70         80         90        100        110        120 
GGEQVAINAE IEEEARFEPQ DIPLDIVYED EDIIIINKPR DLVVHPGAGN PDGTVLNALL 

       130        140        150        160        170        180 
HYYPPIADVP RAGIVHRLDK DTTGLMVVAK TVPAQTRLVE SLQRREITRE YEAVAIGHMT 

       190        200        210        220        230        240 
AGGTVDEPIS RHPTKRTHMA VHPMGKPAVT HYRIMEHFRV HTRLRLRLET GRTHQIRVHM 

       250        260        270        280        290        300 
AHITHPLVGD PVYGGRPRPP KGASEAFIST LRKFDRQALH ATMLRLYHPI SGIEMEWHAP 

       310        320 
IPQDMVELIE VMRADFEEHK DEVDWL

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	Ogura T., Tomoyasu T. Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"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: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 271-326. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli, is controlled by a heat shock sigma factor (sigma 32)." Kitagawa M., Wada C., Yoshioka S., Yura T. J. Bacteriol. 173:4247-4253(1991) [PubMed: 1906060] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 40-326. Strain: K12.
[6]	"A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli." Raychaudhuri S., Conrad J., Hall B.G., Ofengand J. RNA 4:1407-1417(1998) [PubMed: 9814761] [Abstract] Cited for: CHARACTERIZATION. Strain: K12 / MG1655 / ATCC 47076.
[7]	"Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD)." Wrzesinski J., Bakin A., Ofengand J., Lane B.G. IUBMB Life 50:33-37(2000) [PubMed: 11087118] [Abstract] Cited for: FUNCTION, PROTEIN SEQUENCE OF N-TERMINUS.
[8]	"A second function for pseudouridine synthases: a point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain." Gutgsell N.S., Del Campo M., Raychaudhuri S., Ofengand J. RNA 7:990-998(2001) [PubMed: 11453071] [Abstract] Cited for: MUTAGENESIS OF ASP-139.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

U50134 Genomic DNA. Translation: AAA92957.1.
U00096 Genomic DNA. Translation: AAC75643.1.
AP009048 Genomic DNA. Translation: BAA16479.2.
X57620 Genomic DNA. No translation available.

PIR

E65037.

RefSeq

AP_003176.1.
NP_417085.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QYU	X-ray	2.00	A	2-325	[»]
1V9F	X-ray	1.70	A	2-325	[»]
2IST	X-ray	1.86	A	2-325	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10721N.

IntAct

P33643. 18 interactions.

Genome annotation databases

GeneID

947087.

GenomeReviews

Gene locus JW2576 in contig AP009048_GR.
Gene locus b2594 in contig U00096_GR.

KEGG

ecj:JW2576.
eco:b2594.

Organism-specific databases

EchoBASE

EB2022.

EcoGene

EG12098. rluD.

CMR

Search...

Phylogenomic databases

HOGENOM

P33643.

OMA

P33643. KRKITRE.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12098-MON.

Family and domain databases

InterPro

IPR006145. Pseudouridine_synth.
IPR006224. Pseudouridine_synth_CS.
IPR006225. Pseudouridine_synth_RluD.
IPR002942. S4_RNA_bd.
[Graphical view]

Pfam

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

ProDom

PD001819. PseudoU_synth. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00363. S4. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00005. rluA_subfam. 1 hit.

PROSITE

PS01129. PSI_RLU. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

RLUD_ECOLI

Accession

Primary (citable) accession number: P33643
Secondary accession number(s): P77003

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 86 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents