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Interaction information
Interaction summary
Short label
tRNA Pseudouridine Synthase B-5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
Full name
tRNA Pseudouridine Synthase B interacts with 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
Source database
RCSB PDB ID
Date modified
2011-03-25 21:11:08 JST
Protein information
Short label
tRNA Pseudouridine Synthase B
Full name
Chain A of model 1K8W: tRNA Pseudouridine Synthase B
Gene
truB (tRNA U55 pseudouridine synthase)
GeneID
Official symbol
truB
Synonyms
3 synonym(s)
Description
tRNA U55 pseudouridine synthase
Ontologies
2 ontology(s)
Functions
0 function(s)
Processes
1 process(s)
GO:0009451
RNA modification
Evidence
n/a
Term ID
Name
RNA modification
Namespace
biological_process
Definition
The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically." [GOC:go_curators, ISBN:1555811337 "Modification and Editing of RNA
Synonyms
1 synonym(s)
Is-a
2 item(s)
GO:0016070
RNA metabolic process
GO:0043412
macromolecule modification
Components
1 component(s)
GO:0005737
cytoplasm
Evidence
n/a
Term ID
Name
cytoplasm
Namespace
cellular_component
Definition
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
Is-a
1 item(s)
GO:0044424
intracellular part
Origin
Escherichia coli
NCBI Taxonomy ID
Name
Escherichia coli
Synonyms
16 synonym(s).
"Bacillus coli" Migula 1895
"Bacterium coli commune" Escherich 1885
"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Escherichia coli (Migula 1895) Castellani and Chalmers 1919
Escherichia coli retron Ec107
Escherichia coli retron Ec67
Escherichia coli retron Ec79
Escherichia coli retron Ec86
Eschericia coli
bacterium 10a
bacterium E3
Cross references
1 item(s)
UniProt
Sequence
RNA information
Short label
5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
Full name
Chain B of model 1K8W: 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'
Sequence
Experiments (1)
Experiment 1
hoang-2001
Full name
X-ray diffraction
Detection method
x-ray crystallography (MI:0114)
Term ID
Name
x-ray crystallography
Definition
Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallisation conditions.
Synonyms
2 synonym(s)
X-ray (PSI-MI-alternate)
x-ray diffraction (PSI-MI-short)
Is-a
2 item(s)
MI:0013
biophysical
MI:0659
experimental feature detection
Host organisms
1 host organism(s)
Origin
Escherichia coli
NCBI Taxonomy ID
Name
Escherichia coli
Synonyms
16 synonym(s).
"Bacillus coli" Migula 1895
"Bacterium coli commune" Escherich 1885
"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Escherichia coli (Migula 1895) Castellani and Chalmers 1919
Escherichia coli retron Ec107
Escherichia coli retron Ec67
Escherichia coli retron Ec79
Escherichia coli retron Ec86
Eschericia coli
bacterium 10a
bacterium E3
Reference
HOANG, C, et al. , Cell 2001 Dec;107(7):929-39
PMID
Title
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Authors
HOANG, C, et al.
HOANG, C
FERRé-D'AMARé, A R
Citation
Cell 2001 Dec;107(7):929-39
References (1)
Reference 1
HOANG, C, et al. , Cell 2001 Dec;107(7):929-39
PMID
Title
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Authors
HOANG, C, et al.
HOANG, C
FERRé-D'AMARé, A R
Citation
Cell 2001 Dec;107(7):929-39
Related articles (1)
Article 1
HOANG, C, et al. , Cell 2001 Dec;107(7):929-39
PMID
Title
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Authors
HOANG, C, et al.
HOANG, C
FERRé-D'AMARé, A R
Citation
Cell 2001 Dec;107(7):929-39
Attributes (3)
Attributes
3 attribute(s)
3d-structure
Crystal structure of the E. coli pseudouridine synthase TruB bound to a T stem-loop RNA
3d-resolution
1.85A
3d-r-factors
working 18.400%, free 21.100%
1K8W
947687
GO:0009451
562
P60340
1K8WA:tRNA Pseudouridine Synthase B
MI:0114
11779468