rihC:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
ribonucleoside hydrolase 3<ref name='LIB:Riley_2006'/>, YaaF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RihC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0030<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''ribonucleoside hydrolase 3<ref name='LIB:Riley_2006'/>, YaaF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RihC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0030<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0031, JW0028, yaaF, b0030''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.- 3.2.2.-]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.- 3.2.2.-]<ref name='LIB:Riley_2006'/>


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46aa167998136"  class=" tableEdit GO_table_product dataTable"   
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!|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:0016798
GO:0005737
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|
hydrolase activity, acting on glycosyl bonds
cytoplasm
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|
GO_REF:0000004<br />GO_REF:0000020
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
SP_KW:KW-0326<br />HAMAP:MF_01432
 
|
|
F
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
|
complete
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0016787
GO:0009226
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|
hydrolase activity
nucleotide-sugar biosynthetic process
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|
GO_REF:0000004
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
SP_KW:KW-0378
 
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
|
complete
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0008152
GO:0006144
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|
metabolic process
purine base metabolic process
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|
GO_REF:0000004
GOA:hamap<br />GO_REF:0000020
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
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SP_KW:KW-0326
HAMAP:MF_01432
|
|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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pyrimidine base metabolic process
pyrimidine base metabolic process
|
|
GO_REF:0000020
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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GO:0006144
GO:0008152
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|
purine base metabolic process
metabolic process
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GO_REF:0000020
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
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HAMAP:MF_01432
SP_KW:KW-0326
|
|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016787
|
hydrolase activity
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0378
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F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0016798
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|
cytoplasm
hydrolase activity, acting on glycosyl bonds
|
|
GOA:hamap<br />GO_REF:0000020
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|
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01432
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|
C
F
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|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
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|
required fields missing 
complete
|-  
|-  
|
|
 
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GO:0009226
GO:0016798
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nucleotide-sugar biosynthetic process
hydrolase activity, acting on glycosyl bonds
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0326
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|
P
F
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|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
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required fields missing 
complete
|-  
|-  
|
|
 
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GO:0015949
GO:0006974
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|
nucleobase, nucleoside and nucleotide interconversion
response to DNA damage stimulus
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PMID:11967071
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IEP: Inferred from Expression Pattern
|
|
 
|
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P  
P
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|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
 
|
|
required fields missing 
complete


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


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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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IEIVMCGLDV TNQAILTPDY LSTLPQLNRT GKMLHALFSH YRSGSMQSGL RMHDLCAIAW
IEIVMCGLDV TNQAILTPDY LSTLPQLNRT GKMLHALFSH YRSGSMQSGL RMHDLCAIAW
LVRPDLFTLK PCFVAVETQG EFTSGTTVVD IDGCLGKPAN VQVALDLDVK GFQQWVAEVL ALAS</pre>  
LVRPDLFTLK PCFVAVETQG EFTSGTTVVD IDGCLGKPAN VQVALDLDVK GFQQWVAEVL ALAS</pre>  
|-
!align=left {{table heading style}} |Length
||
304
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
32.56 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
32.56 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.2 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
22460 - 23460 (calc based on 4 Y, 3 W, and 8 C residues)  
22,460 - 23,460 (calc based on 4 Y, 3 W, and 8 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46aa16831188b"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
2..304
|
[http://pfam.janelia.org/family/PF01156 PF01156  Inosine-uridine preferring nucleoside hydrolase]
|


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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


<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>rihC
<beststructure>
562</beststructure>
gene=rihC
 
taxon=562,83333
</beststructure>
|-
|-
!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=rihC&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P22564 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=rihC&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P22564 PSI-PRED (P22564)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P22564 Genomes TO Protein (P22564)] (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_notes--></protect>
</td><td></protect>
==== 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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|- {{table_heading_style}}
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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/16128024 GI:16128024]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11082-MONOMER EcoCyc:EG11082-MONOMER]
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[[ASAP]]
|
ASAP:ABE-0000109
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P22564 UniProtKB/Swiss-Prot:P22564]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11082
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P22564 SwissModel:P22564]
EcoGene:EG11082
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[[uniprot:P22564|UniProt:P22564]]
[http://www.ncbi.nlm.nih.gov/gene?term=944796 GeneID:944796]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF01156 PFAM:PF01156]
[http://www.ncbi.nlm.nig.gov/protein/Array GeneID:944796]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414571 RefSeq:NP_414571]
RegulonDB:ECK120001070
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P22564 ModBase:P22564]
EchoBASE:EB1074
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0009226_!_nucleotide-sugar biosynthetic process]][[Category:GO:0015949_!_nucleobase, nucleoside and nucleotide interconversion]]

Latest revision as of 20:19, 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

RihC

Synonyms

ribonucleoside hydrolase 3[1], YaaF[2][1], RihC[2][1], B0030[2][1] , ECK0031, JW0028, yaaF, b0030

Product description

ribonucleoside hydrolase 3[2][3]

Ribonucleoside hydrolase[4]

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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0009226

nucleotide-sugar biosynthetic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0006144

purine base metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01432

P

Seeded from EcoCyc (v14.0)

complete

GO:0006206

pyrimidine base metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01432

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01432

F

Seeded from EcoCyc (v14.0)

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071[5]

IEP: Inferred from Expression Pattern

P

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 

MRLPIFLDTD PGIDDAVAIA AAIFAPELDL QLMTTVAGNV SVEKTTRNAL QLLHFWNAEI
PLAQGAAVPL VRAPRDAASV HGESGMAGYD FVEHNRKPLG IPAFLAIRDA LMRAPEPVTL
VAIGPLTNIA LLLSQCPECK PYIRRLVIMG GSAGRGNCTP NAEFNIAADP EAAACVFRSG
IEIVMCGLDV TNQAILTPDY LSTLPQLNRT GKMLHALFSH YRSGSMQSGL RMHDLCAIAW
LVRPDLFTLK PCFVAVETQG EFTSGTTVVD IDGCLGKPAN VQVALDLDVK GFQQWVAEVL ALAS
Length

304

Mol. Wt

32.56 kDa

pI

5.2 (calculated)

Extinction coefficient

22,460 - 23,460 (calc based on 4 Y, 3 W, and 8 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

2..304

PF01156 Inosine-uridine preferring nucleoside hydrolase

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=rihC 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:16128024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000109

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P22564

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11082

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11082

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944796

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944796

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001070

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1074

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 1.4 1.5 1.6 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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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