nei:Gene Product(s): Difference between revisions

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*  
*  
****************************************************************************************** -->{{Product_nomenclature_help}}
****************************************************************************************** -->{{Product_nomenclature_help}}
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
endonuclease VIII<ref name='LIB:Riley_2006'/>, 5-formyluracil/5-hydroxymethyluracil DNA glycosylase<ref name='LIB:Riley_2006'/>, B0714<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Nei<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''endonuclease VIII<ref name='LIB:Riley_2006'/>, 5-formyluracil/5-hydroxymethyluracil DNA glycosylase<ref name='LIB:Riley_2006'/>, B0714<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Nei<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0703, JW0704, b0714''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 56: Line 56:
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.-.- 3.2.-.-]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.-.- 3.2.-.-]<ref name='LIB:Riley_2006'/>


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*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46aa3ee6140ce"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
|- {{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
|-  
|-  
|
|
Line 86: Line 86:
oxidized pyrimidine base lesion DNA N-glycosylase activity
oxidized pyrimidine base lesion DNA N-glycosylase activity
|
|
GO_REF:0000020
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 94: Line 94:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 105: Line 105:
nucleic acid binding
nucleic acid binding
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 113: Line 113:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 124: Line 124:
DNA binding
DNA binding
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR015886<br />SP_KW:KW-0238
InterPro:IPR015887
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003677
|
DNA binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0238
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 143: Line 162:
damaged DNA binding
damaged DNA binding
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 151: Line 170:
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003684
|
damaged DNA binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR015886
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003824
|
catalytic activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR010663
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 162: Line 219:
catalytic activity
catalytic activity
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0511
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR015886<br />SP_KW:KW-0511
HAMAP:MF_01253
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 181: Line 257:
DNA-(apurinic or apyrimidinic site) lyase activity
DNA-(apurinic or apyrimidinic site) lyase activity
|
|
GO_REF:0000003<br />GO_REF:0000020
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
EC:4.2.99.18<br />HAMAP:MF_01253
InterPro:IPR000214
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012319
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR015886
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR015887
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
GOA:spec<br />GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:4.2.99.18
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
PMID:10862773
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0006281
|
DNA repair
|
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_01253
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008270
|
zinc ion binding
|
PMID:16145054
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0006281
|
DNA repair
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000214
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 200: Line 428:
DNA repair
DNA repair
|
|
GO_REF:0000002<br />GO_REF:0000004<br />GO_REF:0000020
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000214<br />SP_KW:KW-0234<br />HAMAP:MF_01253
InterPro:IPR015887
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003684
|
damaged DNA binding
|
PMID:17002303
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0003684
|
damaged DNA binding
|
PMID:10862773
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0006281
|
DNA repair
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0234
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 219: Line 504:
base-excision repair
base-excision repair
|
|
GO_REF:0000002
PMID:17002303
|
IDA: Inferred from Direct Assay
|
 
|
P
|
 
|
complete
|-
|
 
|
GO:0006284
|
base-excision repair
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 227: Line 531:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003906
|
DNA-(apurinic or apyrimidinic site) lyase activity
|
PMID:17002303
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
|
complete  
complete  
Line 238: Line 561:
nucleotide-excision repair
nucleotide-excision repair
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 246: Line 569:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 257: Line 580:
response to DNA damage stimulus
response to DNA damage stimulus
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 265: Line 588:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 276: Line 599:
metabolic process
metabolic process
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 284: Line 607:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 295: Line 618:
zinc ion binding
zinc ion binding
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000214<br />InterPro:IPR012319<br />InterPro:IPR015886<br />SP_KW:KW-0862
InterPro:IPR000214
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 310: Line 633:


|
|
GO:0008534
GO:0008270
|
|
oxidized purine base lesion DNA N-glycosylase activity
zinc ion binding
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 322: Line 645:
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 329: Line 652:


|
|
GO:0016787
GO:0008270
|
|
hydrolase activity
zinc ion binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0378
InterPro:IPR015886
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 348: Line 671:


|
|
GO:0016798
GO:0008270
|
|
hydrolase activity, acting on glycosyl bonds
zinc ion binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0326
InterPro:IPR015887
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 367: Line 690:


|
|
GO:0016829
GO:0008270
|
|
lyase activity
zinc ion binding
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0456
SP_KW:KW-0862
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 386: Line 709:


|
|
GO:0046872
GO:0016787
|
|
metal ion binding
hydrolase activity
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0479
SP_KW:KW-0378
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0016798
|
|
cytoplasm
hydrolase activity, acting on glycosyl bonds
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0326
|
|
C
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
Line 428: Line 751:
hydrolase activity, hydrolyzing N-glycosyl compounds
hydrolase activity, hydrolyzing N-glycosyl compounds
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000214<br />InterPro:IPR012319<br />InterPro:IPR015886<br />InterPro:IPR015887
InterPro:IPR000214
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 443: Line 766:


|
|
GO:0003906
GO:0016799
|
hydrolase activity, hydrolyzing N-glycosyl compounds
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012319
|
|
DNA-(apurinic or apyrimidinic site) lyase activity
F
|
|
PMID:10862773
Seeded from [[EcoCyc]] (v14.0)
|
|
IDA: Inferred from Direct Assay
complete
|-
|
|


|
GO:0016799
|
hydrolase activity, hydrolyzing N-glycosyl compounds
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR015886
|
|
F
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|


|
GO:0016799
|
hydrolase activity, hydrolyzing N-glycosyl compounds
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR015887
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 462: Line 823:


|
|
GO:0008270
GO:0016829
|
|
zinc ion binding
lyase activity
|
|
PMID:16145054
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
SP_KW:KW-0456
|
|
F
F
|
|
 
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 481: Line 842:


|
|
GO:0003684
GO:0046872
|
|
damaged DNA binding
metal ion binding
|
|
PMID:10862773
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
SP_KW:KW-0479
|
|
F
F
|
|
 
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  


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*  
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****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46aa3ef0582ce"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 645: Line 1,006:
|
|
Experiment(s):EBI-1137778<br />  
Experiment(s):EBI-1137778<br />  
|-
|
Protein
|
rplU
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpsD
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rpmB
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
groL
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
slyD
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
groS
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
rplD
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
hupB
|
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
nfi
|
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):21.173437
|-
|
DNA
|
8-oxoG containing substrates
|
Substrate
|
PMID:17002303
|
X-linking
|-
|
DNA
|
Tetrahydrofuran analogs
|
Substrate-processes to a gap
|
PMID:17002303
|
Glycosylase assay
|-
|
DNA
|
cis-(5S,6R)-thymine glycol (TgA)
|
Substrate
|
PMID:17002303
|
Binding assays
|-
|
DNA
|
cis-(5R,6S)-thymine glycol (TgC)
|
Substrate
|
PMID:17002303
|
Binding assays
|-
|
DNA
|
5,6-dihydrouracil (DHU)
|
Substrate
|
PMID:17002303
|
Binding assay


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32,430 - 32,930 (calc based on 7 Y, 4 W, and 4 C residues)
32,430 - 32,930 (calc based on 7 Y, 4 W, and 4 C residues)


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Removed
Removed
|
|
[http://www.uniprot.org/uniprot/P50465#section_features UniProt:P50465]  
[http://www.uniprot.org/uniprot/P50465#section_features UniProt:P50465]
|
|-
|
Domain
|
2..111
|
[http://pfam.janelia.org/family/PF01149 PF01149  Formamidopyrimidine-DNA glycosylase N-terminal domain]
|
 
|
PMID:19920124
|-
|
Domain
|
235..263
|
[http://pfam.janelia.org/family/PF06827 PF06827  Zinc finger found in FPG and IleRS]
|


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PMID:19920124
|-
|
Domain
|
126..215
|
[http://pfam.janelia.org/family/PF06831 PF06831  Formamidopyrimidine-DNA glycosylase H2TH domain]
|
 
|
PMID:19920124
 
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||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P50465 Protein Model Portal]
* [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/genome3d/read?uniprot_id=P50465 PSI-PRED (P50465)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P50465 Genomes TO Protein (P50465)] (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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</td><tr><table><!--Structure_notes--></protect>
===Notes===
===Notes===
* Kinetic properties of Nei are described in <ref name='PMID:10862773'/>
* Kinetic properties of Nei are described in <ref name='PMID:10862773'/> and <ref name='PMID:17002303'/>
* Structures of active and inactive mutants described in <ref name='PMID:16145054'/>
* Structures of active and inactive mutants described in <ref name='PMID:16145054'/>
* Catalytically important residues E2 and R252
* Catalytically important residues E2 and R252
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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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6383-MONOMER EcoCyc:G6383-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16128689 GI:16128689]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_415242.1 GeneID:945320]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0002433
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P50465 UniProtKB/Swiss-Prot:P50465]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6383
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG13237
|
''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:P50465|UniProt:P50465]]
[http://www.ncbi.nlm.nih.gov/gene?term=945320 GeneID:945320]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF01149 PFAM:PF01149]
RegulonDB:ECK120002983
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415242 RefSeq:NP_415242]
EchoBASE:EB3026
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments


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{{BacktoTop}}
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006281_!_DNA repair]][[Category:Products with structures in PDB]]

Latest revision as of 20:29, 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

Nei

Synonyms

endonuclease VIII[1], 5-formyluracil/5-hydroxymethyluracil DNA glycosylase[1], B0714[2][1], Nei[2][1] , ECK0703, JW0704, b0714

Product description

endonuclease VIII[2][3]

DNA glycosylase/apurinic lyase, deoxyinosine-specific; endonuclease VIII[4]

EC number (for enzymes)
edit table


Notes

Function

[back to top]


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:0000703

oxidized pyrimidine base lesion DNA N-glycosylase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01253

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010979

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015887

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

F

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015886

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010663

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0511

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01253

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000214

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015886

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015887

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.2.99.18

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

PMID:10862773[5]

IDA: Inferred from Direct Assay

F

complete

GO:0006281

DNA repair

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01253

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:16145054[6]

IDA: Inferred from Direct Assay

F

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000214

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015887

P

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

PMID:17002303[7]

IDA: Inferred from Direct Assay

F

complete

GO:0003684

damaged DNA binding

PMID:10862773[5]

IDA: Inferred from Direct Assay

F

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006284

base-excision repair

PMID:17002303[7]

IDA: Inferred from Direct Assay

P

complete

GO:0006284

base-excision repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

P

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

PMID:17002303[7]

IDA: Inferred from Direct Assay

F

complete

GO:0006289

nucleotide-excision repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015886

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

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:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000214

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015886

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015887

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc (v14.0)

complete

GO:0016799

hydrolase activity, hydrolyzing N-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000214

F

Seeded from EcoCyc (v14.0)

complete

GO:0016799

hydrolase activity, hydrolyzing N-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012319

F

Seeded from EcoCyc (v14.0)

complete

GO:0016799

hydrolase activity, hydrolyzing N-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015886

F

Seeded from EcoCyc (v14.0)

complete

GO:0016799

hydrolase activity, hydrolyzing N-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015887

F

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

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

Protein

hupB

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

lpdA

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

groL

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rplD

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rplU

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rpmB

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rpsD

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

rpsN

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

slyD

PMID:15690043[8]

Experiment(s):EBI-882379

Protein

nadE

PMID:16606699[9]

Experiment(s):EBI-1137778

Protein

prs

PMID:16606699[9]

Experiment(s):EBI-1137778

Protein

groL

PMID:16606699[9]

Experiment(s):EBI-1137778

Protein

rplU

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

groL

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

slyD

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

hupB

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

nfi

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):21.173437

DNA

8-oxoG containing substrates

Substrate

PMID:17002303[7]

X-linking

DNA

Tetrahydrofuran analogs

Substrate-processes to a gap

PMID:17002303[7]

Glycosylase assay

DNA

cis-(5S,6R)-thymine glycol (TgA)

Substrate

PMID:17002303[7]

Binding assays

DNA

cis-(5R,6S)-thymine glycol (TgC)

Substrate

PMID:17002303[7]

Binding assays

DNA

5,6-dihydrouracil (DHU)

Substrate

PMID:17002303[7]

Binding assay

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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 

MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKPYQSQL IGQHVTHVET RGKALLTHFS
NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT ILLYSASDIE MLTPEQLTTH
PFLQRVGPDV LDPNLTPEVV KERLLSPRFR NRQFAGLLLD QAFLAGLGNY LRVEILWQVG
LTGNHKAKDL NAAQLDALAH ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGEPCER
CGSIIEKTTL SSRPFYWCPG CQH
Length

263

Mol. Wt

29.845 kDa

pI

8.0 (calculated)

Extinction coefficient

32,430 - 32,930 (calc based on 7 Y, 4 W, and 4 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

Initiator Methionine

1

Removed

UniProt:P50465

Domain

2..111

PF01149 Formamidopyrimidine-DNA glycosylase N-terminal domain

PMID:19920124[11]

Domain

235..263

PF06827 Zinc finger found in FPG and IleRS

PMID:19920124[11]

Domain

126..215

PF06831 Formamidopyrimidine-DNA glycosylase H2TH domain

PMID:19920124[11]

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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=nei taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

  • Kinetic properties of Nei are described in [5] and [7]
  • Structures of active and inactive mutants described in [6]
  • Catalytically important residues E2 and R252

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:16128689

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945320

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002433

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P50465

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6383

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13237

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945320

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002983

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3026

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 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. ↑ 5.0 5.1 5.2 Hazra, TK et al. (2000) Characterization of a novel 8-oxoguanine-DNA glycosylase activity in Escherichia coli and identification of the enzyme as endonuclease VIII. J. Biol. Chem. 275 27762-7 PubMed
  6. ↑ 6.0 6.1 Golan, G et al. (2005) Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Nucleic Acids Res. 33 5006-16 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 Kropachev, KY et al. (2006) Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Biochemistry 45 12039-49 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ 9.0 9.1 9.2 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 10.8 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  11. ↑ 11.0 11.1 11.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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