truD:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

TruD

Synonyms

pseudoruidine synthase[1], B2745[2][1], YgbO[2][1], TruD[2][1] , ECK2740, JW2715, ygbO, b2745

Product description

tRNA pseudouridine 13 synthase[2][3]

tRNA(Glu) U13 pseudouridine synthase[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001656

P

Seeded from EcoCyc (v14.0)

complete

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011760

P

Seeded from EcoCyc (v14.0)

complete

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020103

P

Seeded from EcoCyc (v14.0)

complete

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020119

P

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001656

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011760

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020103

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020119

F

Seeded from EcoCyc (v14.0)

complete

GO:0008033

tRNA processing

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0819

P

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01082

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001656

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011760

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020103

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020119

F

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0031119

tRNA pseudouridine synthesis

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01082

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

matC

PMID:16606699[5]

Experiment(s):EBI-1143804

Protein

cysQ

PMID:16606699[5]

Experiment(s):EBI-1143804

Protein

nohB

PMID:16606699[5]

Experiment(s):EBI-1143804

Protein

rplB

PMID:16606699[5]

Experiment(s):EBI-1143804

Protein

metG

PMID:16606699[5]

Experiment(s):EBI-1143804

Protein

nohA

PMID:16606699[5]

Experiment(s):EBI-1143804
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MIEFDNLTYL HGKPQGTGLL KANPEDFVVV EDLGFEPDGE GEHILVRILK NGCNTRFVAD
ALAKFLKIHA REVSFAGQKD KHAVTEQWLC ARVPGKEMPD LSAFQLEGCQ VLEYARHKRK
LRLGALKGNA FTLVLREVSN RDDVEQRLID ICVKGVPNYF GAQRFGIGGS NLQGAQRWAQ
TNTPVRDRNK RSFWLSAARS ALFNQIVAER LKKADVNQVV DGDALQLAGR GSWFVATTEE
LAELQRRVND KELMITAALP GSGEWGTQRE ALAFEQAAVA AETELQALLV REKVEAARRA
MLLYPQQLSW NWWDDVTVEI RFWLPAGSFA TSVVRELINT TGDYAHIAE
Length

349

Mol. Wt

39.091 kDa

pI

6.5 (calculated)

Extinction coefficient

56,950 - 57,450 (calc based on 5 Y, 9 W, and 4 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

1..337

PF01142 tRNA pseudouridine synthase D (TruD)

PMID:19920124[6]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=truD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130652

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947214

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009011

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q57261

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7422

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13109

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947214

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003987

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2912

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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