rsmF:Gene Product(s): Difference between revisions

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|-
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!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
YebU product, m<sup>5</sup>C methyltransferase
YebU, m<sup>5</sup>C methyltransferase
|-
|-
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted methyltransferase product<ref name='LIB:Riley_2006'/>, B1835 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YebU product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RsmF product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted methyltransferase<ref name='LIB:Riley_2006'/>, B1835<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YebU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RsmF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1834, JW5301, yebU, b1835''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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methyltransferase gene rsmF.
methyltransferase gene rsmF.


16S rRNA m(5)C1407 methyltransferase, SAM-dependent<ref name='LIB:EcoGene'/>
|-
|-
!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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*


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===Notes===
===Notes===
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{{BacktoTop}}
{{BacktoTop}}
<protect>
<protect>
<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.23767.C46aa8076cb440-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.23767.C46aa8076cb440-->
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|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|
 
|
GO:0003723
|
RNA binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011023
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003723
|
RNA binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR018314
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003723
|
RNA binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0694
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01579
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0963
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|-  
|
|
 
|
|
[[Category:GO:0031167_!_rRNA_methylation]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0031167_!_rRNA_methylation GO:0031167]
GO:0005737
|
|
rRNA methylation
cytoplasm
|
|
GO_REF:0000023
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_SL:SL-0086
|
|
P
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
|
[[Category:GO:0016434_!_rRNA_(cytosine)_methyltransferase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016434_!_rRNA_(cytosine)_methyltransferase_activity GO:0016434]
GO:0070475
|
|
rRNA (cytosine) methyltransferase activity
rRNA base methylation
|
|
PMID:16678201
|
|
IMP: Inferred from Mutant Phenotype
|
|
 
|
|
F
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete


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!|Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence


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===Notes===
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
||


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QRDKELWLFP VGIEALIGKV RFSRLGIKLA ETHNKGYRWQ HEAVIALASP DNMNAFELTP
QRDKELWLFP VGIEALIGKV RFSRLGIKLA ETHNKGYRWQ HEAVIALASP DNMNAFELTP
QEAEEWYRGR DVYPQAAPVA DDVLVTFQHQ PIGLAKRIGS RLKNSYPREL VRDGKLFTGN A</pre>  
QEAEEWYRGR DVYPQAAPVA DDVLVTFQHQ PIGLAKRIGS RLKNSYPREL VRDGKLFTGN A</pre>  
|-
!align=left {{table heading style}} |Length
||
481
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
53.23 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
53.44 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.4 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
71390 - 72265 (calc based on 11 Y, 10 W, and 7 C residues)  
71,390 - 72,265 (calc based on 11 Y, 10 W, and 7 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.23767.E46aa8081557a0-->
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
29..209
|
[http://pfam.janelia.org/family/PF01189 PF01189  NOL1/NOP2/sun family]
|
 
|
PMID:19920124
|-
|
Domain
|
199..479
|
[http://pfam.janelia.org/family/PF01189 PF01189  NOL1/NOP2/sun family]
|


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<td>
<!-- motifs column 2-->
<motif_map/>
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<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>rsmF
<beststructure>
562</beststructure>
gene=rsmF
 
taxon=562,83333
</beststructure>
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|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=rsmF&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P76273 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=rsmF&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76273 PSI-PRED (P76273)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76273 Genomes TO Protein (P76273)] (GTOP)
* [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)


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==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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===Notes===
===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/90111341 GI:90111341]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7008-MONOMER EcoCyc:G7008-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/protein/NP_416349.2 GeneID:946348]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0006106
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P76273 UniProtKB/Swiss-Prot:P76273]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoCyc]]
|
|
[[uniprot:P76273|UniProt:P76273]]
EcoCyc:G7008
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[EcoGene]]
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[http://pfam.sanger.ac.uk/family?acc=PF01189 PFAM:PF01189]
EcoGene:EG14023
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416349 RefSeq:NP_416349]
[http://www.ncbi.nlm.nih.gov/gene?term=946348 GeneID:946348]
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Escherichia coli str. K-12 substr. MG1655
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[RegulonDB]]
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[http://salilab.org/modbase/searchbyid?databaseID=P76273 ModBase:P76273]
RegulonDB:ECK120003595
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2FRX PDB:2FRX]
EchoBASE:EB3777
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
===Categories===
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[[Category:GO:0031167_!_rRNA methylation]][[Category:GO:0016434_!_rRNA (cytosine) methyltransferase activity]][[Category:Products with structures in PDB]][[category:complex:16S rRNA methyltransferase]]
[[Category:Proteins]]

Latest revision as of 20:43, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
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

YebU, m5C methyltransferase

Synonyms

predicted methyltransferase[1], B1835[2][1], YebU[2][1], RsmF[2][1] , ECK1834, JW5301, yebU, b1835

Product description

16S rRNA m5C1407 specific methyltransferase[3][2][4]. Inactivation of the yebU gene leads to loss of methylation at C1407 in 16 S rRNA, but does not interfere with methylation at C1962 in 23 S rRNA. Purified recombinant YebU protein retains its specificity for C1407 in vitro, and methylates 30 S subunits (but not naked 16 S rRNA or 70 S ribosomes) isolated from yebU knockout strains.[3]. Andersen and Douthwaite suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF.

16S rRNA m(5)C1407 methyltransferase, SAM-dependent[5]

EC number (for enzymes)


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Notes

Function

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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:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011023

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018314

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01579

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0070475

rRNA base methylation

PMID:16678201[3]

IMP: Inferred from Mutant Phenotype

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
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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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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 

MLVAQHTVYF PDAFLTQMRE AMPSTLSFDD FLAACQRPLR RSIRVNTLKI SVADFLQLTA
PYGWTLTPIP WCEEGFWIER DNEDALPLGS TAEHLSGLFY IQEASSMLPV AALFADGNAP
QRVMDVAAAP GSKTTQISAR MNNEGAILAN EFSASRVKVL HANISRCGIS NVALTHFDGR
VFGAAVPEMF DAILLDAPCS GEGVVRKDPD ALKNWSPESN QEIAATQREL IDSAFHALRP
GGTLVYSTCT LNQEENEAVC LWLKETYPDA VEFLPLGDLF PGANKALTEE GFLHVFPQIY
DCEGFFVARL RKTQAIPALP APKYKVGNFP FSPVKDREAG QIRQAATGVG LNWDENLRLW
QRDKELWLFP VGIEALIGKV RFSRLGIKLA ETHNKGYRWQ HEAVIALASP DNMNAFELTP
QEAEEWYRGR DVYPQAAPVA DDVLVTFQHQ PIGLAKRIGS RLKNSYPREL VRDGKLFTGN A
Length

481

Mol. Wt

53.44 kDa

pI

5.4 (calculated)

Extinction coefficient

71,390 - 72,265 (calc based on 11 Y, 10 W, and 7 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

29..209

PF01189 NOL1/NOP2/sun family

PMID:19920124[6]

Domain

199..479

PF01189 NOL1/NOP2/sun family

PMID:19920124[6]

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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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:90111341

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946348

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006106

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76273

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7008

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14023

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946348

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003595

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3777

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 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. ↑ 3.0 3.1 3.2 Andersen, NM & Douthwaite, S (2006) YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 777-86 PubMed
  4. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  5. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  6. ↑ 6.0 6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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