Interaction information

Interaction summary

Short label

tRNA delta(2)-isopentenylpyrophosphate transferase-tRNA(Phe)

Full name

tRNA delta(2)-isopentenylpyrophosphate transferase interacts with tRNA(Phe)

Source database

RCSB PDB

ID

2ZXU

Date modified

2011-03-25 19:16:14 JST

Protein information

Short label

tRNA delta(2)-isopentenylpyrophosphate transferase

Full name

Chain A,B of model 2ZXU: tRNA delta(2)-isopentenylpyrophosphate transferase

Gene

miaA (delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase)

GeneID

948690

Official symbol

miaA

Synonyms

3 synonym(s)

• ECK4167
• JW4129
• trpX

Description

delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase

Ontologies

2 ontology(s)

Functions

0 function(s)

Processes

1 process(s)

GO:0009451

RNA modification

Evidence

n/a

Term ID

GO:0009451

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)

• RNA editing (GOC:hjd)

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

GO:0005737

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 K-12

NCBI Taxonomy ID

83333

Name

Escherichia coli K-12

Synonyms

1 synonym(s).

• Escherichia coli K12

Cross references

1 item(s)

UniProt

P16384

Sequence

2ZXUA:tRNA delta(2)-isopentenylpyrophosphate transferase

RNA information

Short label

tRNA(Phe)

Full name

Chain C,D of model 2ZXU: tRNA(Phe)

Gene

gspM (general secretory pathway component, cryptic)

GeneID

6058075

Official symbol

gspM

Description

general secretory pathway component, cryptic

Cross references

1 item(s)

GenBank Nucleotide

169887498

Sequence

2ZXUC:tRNA(Phe)

Experiments (1)

Experiment 1

chimnaronk-2009

Full name

X-ray diffraction

Detection method

x-ray crystallography (MI:0114)

Term ID

MI:0114

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

562

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

CHIMNARONK, Sarin, et al., Biochemistry 2009 Jun;48(23):5057-65

PMID

19435325

Title

Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.

Authors

CHIMNARONK, Sarin, et al.

• CHIMNARONK, Sarin
• FOROUHAR, Farhad
• SAKAI, Junichi
• YAO, Min
• TRON, Cecile M
• ATTA, Mohamed
• FONTECAVE, Marc
• HUNT, John F
• TANAKA, Isao

Citation

Biochemistry 2009 Jun;48(23):5057-65

References (1)

Reference 1

CHIMNARONK, Sarin, et al., Biochemistry 2009 Jun;48(23):5057-65

PMID

19435325

Title

Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.

Authors

CHIMNARONK, Sarin, et al.

• CHIMNARONK, Sarin
• FOROUHAR, Farhad
• SAKAI, Junichi
• YAO, Min
• TRON, Cecile M
• ATTA, Mohamed
• FONTECAVE, Marc
• HUNT, John F
• TANAKA, Isao

Citation

Biochemistry 2009 Jun;48(23):5057-65

Related articles (1)

Article 1

CHIMNARONK, Sarin, et al., Biochemistry 2009 Jun;48(23):5057-65

PMID

19435325

Title

Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.

Authors

CHIMNARONK, Sarin, et al.

• CHIMNARONK, Sarin
• FOROUHAR, Farhad
• SAKAI, Junichi
• YAO, Min
• TRON, Cecile M
• ATTA, Mohamed
• FONTECAVE, Marc
• HUNT, John F
• TANAKA, Isao

Citation

Biochemistry 2009 Jun;48(23):5057-65

Attributes (3)

Attributes

3 attribute(s)

3d-structure

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP

3d-resolution

2.75A

3d-r-factors

working 23.700%, free 28.100%