endA:Gene Product(s): Difference between revisions

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|-
|-
!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
EndA product
EndA  
|-
|-
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
DNA-specific endonuclease I product<ref name='LIB:Riley_2006'/>, B2945 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, EndA product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA-specific endonuclease I<ref name='LIB:Riley_2006'/>, B2945<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, EndA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2940, JW2912, b2945''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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DNA-specific endonuclease I<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
DNA-specific endonuclease I<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


DNA-specific endonuclease I, periplasmic; inhibited by RNA; extensive DNA breakdown<ref name='LIB:EcoGene'/>
|-
|-
!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
||
||
** [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1]<ref name='LIB:Riley_2006'/>


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===Notes===
===Notes===
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{{BacktoTop}}
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<protect>
<protect>
<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.26274.O46aac8773da3e-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.26274.O46aac8773da3e-->
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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
|-  
|-  
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[[Category:GO:0042597_!_periplasmic_space]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0042597_!_periplasmic_space GO:0042597]
GO:0030288
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periplasmic space
outer membrane-bounded periplasmic space
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[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
 
|
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IEA: Inferred from Electronic Annotation
 
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[http://www.uniprot.org/keywords/KW-0574 SP_KW:KW-0574]
 
|
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C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
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Missing: evidence, reference
|-
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|
complete
 
|
GO:0006308
|
DNA catabolic process
|
 
|
 
|
 
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P
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Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
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Missing: evidence, reference
|-  
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|


|
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[[Category:GO:0016787_!_hydrolase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016787_!_hydrolase_activity GO:0016787]
GO:0004518
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hydrolase activity
nuclease activity
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[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0378 SP_KW:KW-0378]
InterPro:IPR007346
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F
F
|
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Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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|
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[[Category:GO:0004530_!_deoxyribonuclease_I_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0004530_!_deoxyribonuclease_I_activity GO:0004530]
GO:0004518
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deoxyribonuclease I activity
nuclease activity
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[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000003 GO_REF:0000003]
GOA:spkw<br />SP_KW:GO_REF:0000004
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.expasy.org/cgi-bin/nicezyme.pl?3.1.21.1 EC:3.1.21.1]
SP_KW:KW-0540
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F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
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complete  
complete  
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|
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[[Category:GO:0004519_!_endonuclease_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0004519_!_endonuclease_activity GO:0004519]
GO:0004519
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endonuclease activity
endonuclease activity
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[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0255 SP_KW:KW-0255]
SP_KW:KW-0255
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|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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[[Category:GO:0004518_!_nuclease_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0004518_!_nuclease_activity GO:0004518]
GO:0004530
|
|
nuclease activity
deoxyribonuclease I activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR007346 InterPro:IPR007346]<br />[http://www.uniprot.org/keywords/KW-0540 SP_KW:KW-0540]
EC:3.1.21.1
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
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[[Category:GO:0030288_!_outer_membrane-bounded_periplasmic_space]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0030288_!_outer_membrane-bounded_periplasmic_space GO:0030288]
GO:0016787
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|
outer membrane-bounded periplasmic space
hydrolase activity
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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-0378
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C
F
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
|
[[Category:GO:0006308_!_DNA_catabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006308_!_DNA_catabolic_process GO:0006308]
GO:0042597
|
|
DNA catabolic process
periplasmic space
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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-0574
|
|
P
C
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
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[[Category:GO:0000737_!_DNA_catabolic_process,_endonucleolytic]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0000737_!_DNA_catabolic_process,_endonucleolytic GO:0000737]
GO:0042597
|
|
DNA catabolic process, endonucleolytic
periplasmic space
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|
GO_REF:0000023
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IEA: Inferred from Electronic Annotation
|
|
SP_SL:SL-0200
|
|
P
C
|
|
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!!References
!|Partner Type!!Partner!!Notes!!References!!Evidence


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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46aac87f198f5"  class=" tableEdit Product_localization_table"   
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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Periplasm
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PMID:7867949
|
[http://www.york.ac.uk/res/thomas/Echolocation.cfm?EB_SubLocID=EB1312 EchoLocation:endA]
|
 
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!align=left {{table heading style}} |Name
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NLQPSVGEVN GDRGNFMYSQ WNGGEGQYGQ CAMKVDFKEK AAEPPARARG AIARTYFYMR
NLQPSVGEVN GDRGNFMYSQ WNGGEGQYGQ CAMKVDFKEK AAEPPARARG AIARTYFYMR
DQYNLTLSRQ QTQLFNAWNK MYPVTDWECE RDERIAKVQG NHNPYVQRAC QARKS</pre>  
DQYNLTLSRQ QTQLFNAWNK MYPVTDWECE RDERIAKVQG NHNPYVQRAC QARKS</pre>  
|-
!align=left {{table heading style}} |Length
||
235
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
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26.71 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
26.707 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
9.4 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
56380 - 57380 (calc based on 12 Y, 7 W, and 8 C residues)  
56,380 - 57,380 (calc based on 12 Y, 7 W, and 8 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=421aa90e079fa326b6494f812ad13e79.26274.F46aac8812b3c3-->
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
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[http://www.uniprot.org/uniprot/P25736#section_features UniProt:P25736]  
[http://www.uniprot.org/uniprot/P25736#section_features UniProt:P25736]
|
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Domain
|
20..230
|
[http://pfam.janelia.org/family/PF04231 PF04231  Endonuclease I]
|


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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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</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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|-
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!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>endA
<beststructure>
562</beststructure>
gene=endA
 
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=endA&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P25736 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=endA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P25736 PSI-PRED (P25736)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P25736 Genomes TO Protein (P25736)] (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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===Notes===
===Notes===


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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/16130846 GI:16130846]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11336-MONOMER EcoCyc:EG11336-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/NP_417420.1 GeneID:949092]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0009661
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P25736 UniProtKB/Swiss-Prot:P25736]
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Escherichia coli str. K-12 substr. MG1655
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[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoCyc]]
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[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P25736 SwissModel:P25736]
EcoCyc:EG11336
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
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[[uniprot:P25736|UniProt:P25736]]
EcoGene:EG11336
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF04231 PFAM:PF04231]
[http://www.ncbi.nlm.nih.gov/gene?term=949092 GeneID:949092]
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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_417420 RefSeq:NP_417420]
RegulonDB:ECK120001307
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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=P25736 ModBase:P25736]
EchoBASE:EB1312
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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__NOTOC__
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</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0030288_!_outer membrane-bounded periplasmic space]][[Category:GO:0006308_!_DNA catabolic process]][[Category:GO:0000737_!_DNA catabolic process, endonucleolytic]][[Category:Location:periplasm]]

Latest revision as of 20:57, 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

EndA

Synonyms

DNA-specific endonuclease I[1], B2945[2][1], EndA[2][1] , ECK2940, JW2912, b2945

Product description

DNA-specific endonuclease I[2][3]

DNA-specific endonuclease I, periplasmic; inhibited by RNA; extensive DNA breakdown[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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0006308

DNA catabolic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0004518

nuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007346

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0004530

deoxyribonuclease I activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.21.1

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:0042597

periplasmic space

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0574

C

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0200

C

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

periplasm

Periplasm

PMID:7867949[5]

EchoLocation:endA


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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 

MYRYLSIAAV VLSAAFSGPA LAEGINSFSQ AKAAAVKVHA DAPGTFYCGC KINWQGKKGV
VDLQSCGYQV RKNENRASRV EWEHVVPAWQ FGHQRQCWQD GGRKNCAKDP VYRKMESDMH
NLQPSVGEVN GDRGNFMYSQ WNGGEGQYGQ CAMKVDFKEK AAEPPARARG AIARTYFYMR
DQYNLTLSRQ QTQLFNAWNK MYPVTDWECE RDERIAKVQG NHNPYVQRAC QARKS
Length

235

Mol. Wt

26.707 kDa

pI

9.4 (calculated)

Extinction coefficient

56,380 - 57,380 (calc based on 12 Y, 7 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

motif

1-22

UniProt Manual:Signal Peptides

UniProt:P25736

Domain

20..230

PF04231 Endonuclease I

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=endA 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:16130846

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949092

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009661

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P25736

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11336

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11336

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949092

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001307

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1312

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 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. ↑ Jekel, M & Wackernagel, W (1995) The periplasmic endonuclease I of Escherichia coli has amino-acid sequence homology to the extracellular DNases of Vibrio cholerae and Aeromonas hydrophila. Gene 154 55-9 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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