Interaction information

Interaction summary

Short label

Rho transcription termination factor-5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'

Full name

Rho transcription termination factor interacts with 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'

Source database

RCSB PDB

ID

1XPO

Date modified

2011-03-25 18:12:00 JST

Protein information

Short label

Rho transcription termination factor

Full name

Chain A,B,C,D,E,F of model 1XPO: Rho transcription termination factor

Gene

mmoX (methane monooxygenase, A subunit, alpha chain)

GeneID

3104807

Official symbol

mmoX

Description

methane monooxygenase, A subunit, alpha chain

Ontologies

4 ontology(s)

Functions

1 function(s)

GO:0015049

[ISS] methane monooxygenase activity

Evidence

ISS

References

1 reference(s)

PubMed

WARD, Naomi, et al., PLoS Biol. 2004 Oct;2(10):e303

PMID

15383840

Title

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Authors

WARD, Naomi, et al.

• WARD, Naomi
• LARSEN, Øivind
• SAKWA, James
• BRUSETH, Live
• KHOURI, Hoda
• DURKIN, A Scott
• DIMITROV, George
• JIANG, Lingxia
• SCANLAN, David
• KANG, Katherine H
• LEWIS, Matt
• NELSON, Karen E
• METHé, Barbara
• WU, Martin
• HEIDELBERG, John F
• PAULSEN, Ian T
• FOUTS, Derrick
• RAVEL, Jacques
• TETTELIN, Hervé
• REN, Qinghu
• READ, Tim
• DEBOY, Robert T
• SESHADRI, Rekha
• SALZBERG, Steven L
• JENSEN, Harald B
• BIRKELAND, Nils Kåre
• NELSON, William C
• DODSON, Robert J
• GRINDHAUG, Svenn H
• HOLT, Ingeborg
• EIDHAMMER, Ingvar
• JONASEN, Inge
• VANAKEN, Susan
• UTTERBACK, Terry
• FELDBLYUM, Tamara V
• FRASER, Claire M
• LILLEHAUG, Johan R
• EISEN, Jonathan A

Citation

PLoS Biol. 2004 Oct;2(10):e303

Term ID

GO:0015049

Name

methane monooxygenase activity

Namespace

molecular_function

Definition

Catalysis of the reaction: methane + NAD(P)H + H+ + O2 = methanol + NAD(P)+ + H2O.

Synonyms

2 synonym(s)

• methane hydroxylase activity (EC:1.14.13.25)
• methane,NAD(P)H:oxygen oxidoreductase (hydroxylating) (EC:1.14.13.25)

Is-a

1 item(s)

GO:0016709

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen

Processes

2 process(s)

GO:0015947

[ISS] methane metabolic process

Evidence

ISS

References

1 reference(s)

PubMed

WARD, Naomi, et al., PLoS Biol. 2004 Oct;2(10):e303

PMID

15383840

Title

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Authors

WARD, Naomi, et al.

• WARD, Naomi
• LARSEN, Øivind
• SAKWA, James
• BRUSETH, Live
• KHOURI, Hoda
• DURKIN, A Scott
• DIMITROV, George
• JIANG, Lingxia
• SCANLAN, David
• KANG, Katherine H
• LEWIS, Matt
• NELSON, Karen E
• METHé, Barbara
• WU, Martin
• HEIDELBERG, John F
• PAULSEN, Ian T
• FOUTS, Derrick
• RAVEL, Jacques
• TETTELIN, Hervé
• REN, Qinghu
• READ, Tim
• DEBOY, Robert T
• SESHADRI, Rekha
• SALZBERG, Steven L
• JENSEN, Harald B
• BIRKELAND, Nils Kåre
• NELSON, William C
• DODSON, Robert J
• GRINDHAUG, Svenn H
• HOLT, Ingeborg
• EIDHAMMER, Ingvar
• JONASEN, Inge
• VANAKEN, Susan
• UTTERBACK, Terry
• FELDBLYUM, Tamara V
• FRASER, Claire M
• LILLEHAUG, Johan R
• EISEN, Jonathan A

Citation

PLoS Biol. 2004 Oct;2(10):e303

Term ID

GO:0015947

Name

methane metabolic process

Namespace

biological_process

Definition

The chemical reactions and pathways involving methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology

Synonyms

1 synonym(s)

• methane metabolism

Is-a

1 item(s)

GO:0043446

cellular alkane metabolic process

GO:0055114

[ISS] oxidation reduction

Evidence

ISS

References

1 reference(s)

PubMed

WARD, Naomi, et al., PLoS Biol. 2004 Oct;2(10):e303

PMID

15383840

Title

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Authors

WARD, Naomi, et al.

• WARD, Naomi
• LARSEN, Øivind
• SAKWA, James
• BRUSETH, Live
• KHOURI, Hoda
• DURKIN, A Scott
• DIMITROV, George
• JIANG, Lingxia
• SCANLAN, David
• KANG, Katherine H
• LEWIS, Matt
• NELSON, Karen E
• METHé, Barbara
• WU, Martin
• HEIDELBERG, John F
• PAULSEN, Ian T
• FOUTS, Derrick
• RAVEL, Jacques
• TETTELIN, Hervé
• REN, Qinghu
• READ, Tim
• DEBOY, Robert T
• SESHADRI, Rekha
• SALZBERG, Steven L
• JENSEN, Harald B
• BIRKELAND, Nils Kåre
• NELSON, William C
• DODSON, Robert J
• GRINDHAUG, Svenn H
• HOLT, Ingeborg
• EIDHAMMER, Ingvar
• JONASEN, Inge
• VANAKEN, Susan
• UTTERBACK, Terry
• FELDBLYUM, Tamara V
• FRASER, Claire M
• LILLEHAUG, Johan R
• EISEN, Jonathan A

Citation

PLoS Biol. 2004 Oct;2(10):e303

Term ID

GO:0055114

Name

oxidation reduction

Namespace

biological_process

Definition

The process of removal or addition of one or more electrons with or without the concomitant removal or addition of a proton or protons.

Synonyms

1 synonym(s)

• oxidoreductase process

Is-a

1 item(s)

GO:0008152

metabolic process

Components

1 component(s)

GO:0015050

[ISS] methane monooxygenase complex

Evidence

ISS

References

1 reference(s)

PubMed

WARD, Naomi, et al., PLoS Biol. 2004 Oct;2(10):e303

PMID

15383840

Title

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Authors

WARD, Naomi, et al.

• WARD, Naomi
• LARSEN, Øivind
• SAKWA, James
• BRUSETH, Live
• KHOURI, Hoda
• DURKIN, A Scott
• DIMITROV, George
• JIANG, Lingxia
• SCANLAN, David
• KANG, Katherine H
• LEWIS, Matt
• NELSON, Karen E
• METHé, Barbara
• WU, Martin
• HEIDELBERG, John F
• PAULSEN, Ian T
• FOUTS, Derrick
• RAVEL, Jacques
• TETTELIN, Hervé
• REN, Qinghu
• READ, Tim
• DEBOY, Robert T
• SESHADRI, Rekha
• SALZBERG, Steven L
• JENSEN, Harald B
• BIRKELAND, Nils Kåre
• NELSON, William C
• DODSON, Robert J
• GRINDHAUG, Svenn H
• HOLT, Ingeborg
• EIDHAMMER, Ingvar
• JONASEN, Inge
• VANAKEN, Susan
• UTTERBACK, Terry
• FELDBLYUM, Tamara V
• FRASER, Claire M
• LILLEHAUG, Johan R
• EISEN, Jonathan A

Citation

PLoS Biol. 2004 Oct;2(10):e303

Term ID

GO:0015050

Name

methane monooxygenase complex

Namespace

cellular_component

Definition

A protein complex that possesses methane monooxygenase activity; dimeric and trimeric complexes have been characterized.

Is-a

2 item(s)

GO:0043234

protein complex

GO:0044464

cell part

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

Cross references

1 item(s)

UniProt

P22869

Sequence

1XPOA:Rho transcription termination factor

RNA information

Short label

5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'

Full name

Chain G,M,H,J,K,L of model 1XPO: 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'

Sequence

1XPOG:5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'

Experiments (1)

Experiment 1

skordalakes-2005

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

SKORDALAKES, Emmanuel, et al., Structure 2005 Jan;13(1):99-109

PMID

15642265

Title

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.

Authors

SKORDALAKES, Emmanuel, et al.

• SKORDALAKES, Emmanuel
• BROGAN, Andrew P
• PARK, Boon Saeng
• KOHN, Harold
• BERGER, James M

Citation

Structure 2005 Jan;13(1):99-109

References (1)

Reference 1

SKORDALAKES, Emmanuel, et al., Structure 2005 Jan;13(1):99-109

PMID

15642265

Title

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.

Authors

SKORDALAKES, Emmanuel, et al.

• SKORDALAKES, Emmanuel
• BROGAN, Andrew P
• PARK, Boon Saeng
• KOHN, Harold
• BERGER, James M

Citation

Structure 2005 Jan;13(1):99-109

Related articles (1)

Article 1

SKORDALAKES, Emmanuel, et al., Structure 2005 Jan;13(1):99-109

PMID

15642265

Title

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.

Authors

SKORDALAKES, Emmanuel, et al.

• SKORDALAKES, Emmanuel
• BROGAN, Andrew P
• PARK, Boon Saeng
• KOHN, Harold
• BERGER, James M

Citation

Structure 2005 Jan;13(1):99-109

Attributes (3)

Attributes

3 attribute(s)

3d-structure

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin

3d-resolution

3.15A

3d-r-factors

working 28.502%, free 30.594%