EcoliWiki - User contributions [en]

PMID:16782065

2010-05-04T01:28:24Z

Kcarter: Fill PMID: Page!

{{RightTOC}}
<protect>
 '''Lee, SJ, Ko, JH, Kang, HY and Lee, Y''' (2006) Coupled expression of MhpE aldolase and MhpF dehydrogenase in Escherichia coli.''Biochem. Biophys. Res. Commun.'' '''346''':1009-15

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>MhpE (4-hydroxy-2-ketovalerate aldolase) and MhpF [acetaldehyde dehydrogenase (acylating)] are responsible for the last two reactions in the 3-(3-hydroxyphenyl)propionate (3-HPP) catabolic pathway in Escherichia coli, which is homologous to the meta-cleavage pathway in Pseudomonas species. Here, we report that the MhpE aldolase is associated with the MhpF dehydrogenase and that MhpF is indispensable for the folding of MhpE. Moreover, our results suggest that the mhpF and mhpE genes are translationally coupled through a reinitiation mechanism. This reinitiation mechanism may function in ensuring that the expression of mhpE occurs only when MhpF is available for the formation of a complex.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16782065 PubMed]
Online version:[http://dx.doi.org/10.1016/j.bbrc.2006.06.009 10.1016/j.bbrc.2006.06.009]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="E4bdf78387948c" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171954.E4bdf78387948c&page=171954&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:16782065

2010-05-04T01:28:24Z

Kcarter: New PMID: Page!

PMID:2664457

2010-05-04T01:01:30Z

Kcarter: Fill PMID: Page!

{{RightTOC}}
<protect>
 '''Ross, TK, Achberger, EC and Braymer, HD''' (1989) Identification of a second polypeptide required for McrB restriction of 5-methylcytosine-containing DNA in Escherichia coli K12.''Mol. Gen. Genet.'' '''216''':402-7

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>The McrB restriction system in Escherichia coli K12 causes sequence-specific recognition and inactivation of DNA containing 5-methylcytosine residues. We have previously located the mcrB gene near hsdS at 99 min on the E. coli chromosome and demonstrated that it encodes a 51 kDa polypeptide required for restriction of M.AluI methylated (A-G-5mC-T) DNA. We show here, by analysis of maxicell protein synthesis of various cloned fragments from the mcrB region, that a second protein of approximately 39 kDa is also required for McrB-directed restriction. The new gene, designated mcrC, is adjacent to mcrB and located distally to hsdS. The McrB phenotype has been correlated previously with restriction of 5-hydroxy-methyl-cytosine (HMC)-containing T-even phage DNA that lacks the normal glucose modification of HMC, formally designated RglB (for restriction of glucoseless phage). This report reveals a difference between the previously correlated McrB and RglB restriction systems: while both require the mcrB gene product only the McrB system requires the newly identified mcrC-encoded 39-kDa polypeptide.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2664457 PubMed]

|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="S4bdf71ea1a6d5" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171950.S4bdf71ea1a6d5&page=171950&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

2010-05-02T22:27:23Z

Kcarter: Table edited by Kcarter via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|nusA}}{{Tab|Gene|nusA}}{{Tab On|Gene Product(s)|nusA}}{{Tab|Expression|nusA}}{{Tab|Evolution|nusA}}{{Tab|On One Page|nusA}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| id="T46aad5ab1b8f7" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
NusA
|-
!align=left {{table heading style}} |Synonyms
||
transcription termination/antitermination L factor<ref name='LIB:Riley_2006'/>, B3169<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NusA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
|-
!align=left {{table heading style}} |Product description
||
transcription termination/antitermination L factor<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>

Transcription termination/antitermination L factor; mutant survives lambda induction<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||

|- class="tableEdit_footer"
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|}


<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| id="R46aad5ac2b5a7" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0005737
|
cytoplasm
|
PMID:16858726
|
IDA: Inferred from Direct Assay
|

|
C
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0000166
|
nucleotide binding
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR010995
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0003700
|
transcription factor activity
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR013735
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0003723
|
RNA binding
|
GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003029 InterPro:IPR004087 InterPro:IPR004088 InterPro:IPR009019 InterPro:IPR010213 SP_KW:KW-0694
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0005515
|
protein binding
|
GO_REF:0000002 GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR010995 InterPro:IPR013735
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0006350
|
transcription<input name="field[2]" type="hidden" value="transcription" />
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0804
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0006353
|
transcription termination
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0806
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0006355
|
regulation of transcription, DNA-dependent
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0805
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0006950
|
response to stress
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0346
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0030528
|
transcription regulator activity
|
PMID:12161562
|
IDA: Inferred from Direct Assay
|

|
F
|
Fig.2. NusA stimulates pausing of the RNA polymerase at specific sites. Can see on the gel, bands at specific nucleotide sites larger when NusA present.
|
complete
|-
|

|
GO:0031554
|
regulation of transcription termination
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR013735
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0031564
|
transcription antitermination
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0889
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0043565
|
sequence-specific DNA binding
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003583
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0005622
|
intracellular
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003583
|
C
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0030528
|
transcription regulator activity
|
GO_REF:0000002 GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR010213 InterPro:IPR010214
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|

|
GO:0030528
|
transcription regulator activity
|
GO_REF:0000002 GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR010213 InterPro:IPR010214
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete

|- class="tableEdit_footer"
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<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| id="N46aad5b98e068" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
prsA 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rpsD 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rpsG 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
tufA 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
infB 
|

|
PMID:15690043
|
Experiment(s):EBI-886823, EBI-893117 
|-
|
Protein
|
rplA 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rplB 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rplC 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rplD 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rplO 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rplV 
|

|
PMID:15690043
|
Experiment(s):EBI-886823, EBI-893117 
|-
|
Protein
|
rpoA 
|

|
PMID:15690043
|
Experiment(s):EBI-886823, EBI-879354, EBI-883271, EBI-893117 
|-
|
Protein
|
rpoB 
|

|
PMID:15690043
|
Experiment(s):EBI-886823, EBI-879304, EBI-883170, EBI-893117 
|-
|
Protein
|
rpoC 
|

|
PMID:15690043
|
Experiment(s):EBI-886823, EBI-879261, EBI-893117 
|-
|
Protein
|
rpoH 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
rpsC 
|

|
PMID:15690043
|
Experiment(s):EBI-886823 
|-
|
Protein
|
aceE 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
metJ 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
pstS 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
rplS 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
rplX 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
rpsE 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
uspA 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
uvrA 
|

|
PMID:15690043
|
Experiment(s):EBI-893117 
|-
|
Protein
|
infB 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rplS 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpoB 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rplE 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpsD 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpsC 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpsE 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
cybC 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
fur 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpsG 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpoC 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rhsD 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rpsI 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
argG 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
ycgL 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rplP 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rplO 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rplB 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 
|-
|
Protein
|
rplF 
|

|
PMID:16606699
|
Experiment(s):EBI-1145014 

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|}


</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| id="Y46a86918b94f6" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes

|- class="tableEdit_footer"
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<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="K46aad5bb7c086" class=" tableEdit Product_phys_prop_table"

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG10665-MONOMER at EcoCyc]
<pre>MNKEILAVVE AVSNEKALPR EKIFEALESA LATATKKKYE QEIDVRVQID RKSGDFDTFR
RWLVVDEVTQ PTKEITLEAA RYEDESLNLG DYVEDQIESV TFDRITTQTA KQVIVQKVRE
AERAMVVDQF REHEGEIITG VVKKVNRDNI SLDLGNNAEA VILREDMLPR ENFRPGDRVR
GVLYSVRPEA RGAQLFVTRS KPEMLIELFR IEVPEIGEEV IEIKAAARDP GSRAKIAVKT
NDKRIDPVGA CVGMRGARVQ AVSTELGGER IDIVLWDDNP AQFVINAMAP ADVASIVVDE
DKHTMDIAVE AGNLAQAIGR NGQNVRLASQ LSGWELNVMT VDDLQAKHQA EAHAAIDTFT
KYLDIDEDFA TVLVEEGFST LEELAYVPMK ELLEIEGLDE PTVEALRERA KNALATIAQA
QEESLGDNKP ADDLLNLEGV DRDLAFKLAA RGVCTLEDLA EQGIDDLADI EGLTDEKAGA
LIMAARNICW FGDEA</pre>
|-
!align=left {{table heading style}} |Length
||
495
|-
!align=left {{table heading style}} |Mol. Wt
||
54.87 kDa
|-
!align=left {{table heading style}} |pI
||
4.4 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
30,940 - 31,315 (calc based on 6 Y, 4 W, and 3 C residues)

|- class="tableEdit_footer"
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|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| id="S46aad5bbedd21" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.26768.S46aad5bbedd21&page=26768&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || || ||
|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="O46a8691a70e87" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=nusA
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)

|- class="tableEdit_footer"
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|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| id="V46aad5bcbbaa3" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference

|- class="tableEdit_footer"
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===Notes===

==Accessions in Other Databases==
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{{Gene_accessions_help}}
{| id="R46aad5bd280c8" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10665-MONOMER EcoCyc:EG10665-MONOMER]
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[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
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[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AFF6 SwissModel:P0AFF6]
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|-
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[[uniprot:P0AFF6|UniProt:P0AFF6]]
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF00575 PFAM:PF00575]
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|-
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417638 RefSeq:NP_417638]
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===Notes===

==Links==
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{| id="Z46a8691eb3b92" class=" tableEdit Links_table"
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!|Name!!URL!!Comments

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<noinclude>
==References==
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{{RefHelp}}
<references />
__NOTOC__
===Categories===
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[[Category:Proteins]]
[[Category:GO:0006350_!_transcription]][[Category:GO:0006355_!_regulation of transcription, DNA-dependent]][[Category:GO:0005737_!_cytoplasm]]