ddlB:Gene Product(s): Difference between revisions

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{| id="N46aa1b406017e"  class=" tableEdit Product_nomenclature_table"   
{|   id="N46aa1b406017e"  class=" tableEdit Product_nomenclature_table"   


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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
D-alanine:D-alanine ligase<ref name='LIB:Riley_2006'/>, B0092<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Ddl<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DdlB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''D-alanine:D-alanine ligase<ref name='LIB:Riley_2006'/>, B0092<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Ddl<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DdlB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ddl, ECK0093, JW0090, b0092''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  
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****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{| {{Prettytable}} id="R46aa1b41b7235"  class=" tableEdit GO_table_product dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R46aa1b41b7235"  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
|-
|
 
|
GO:0008716
|
D-alanine-D-alanine ligase activity
|
PMID:8756703
|
IMP: Inferred from Mutant Phenotype
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0000166
|
nucleotide binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0547
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|-  
|
|


|
|
GO:0003824
GO:0000287
|
|
catalytic activity
magnesium ion binding
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR011761<br />InterPro:IPR013816<br />InterPro:IPR013817
SP_KW:KW-0460
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008716
|
D-alanine-D-alanine ligase activity
|
PMID:1993184
|
IDA: Inferred from Direct Assay
|
 
|
F
|
Tables II and III
|
|
complete  
complete  
Line 107: Line 164:
ATP binding
ATP binding
|
|
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:IPR011761<br />InterPro:IPR013816<br />InterPro:IPR013817
InterPro:IPR011761
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 122: Line 179:


|
|
GO:0016874
GO:0005524
|
|
ligase activity
ATP binding
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0436
InterPro:IPR013816
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 141: Line 198:


|
|
GO:0009252
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR013817
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR016185
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005524
|
|
peptidoglycan biosynthetic process
ATP binding
|
|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004<br />GO_REF:0000020
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000291<br />InterPro:IPR005905<br />InterPro:IPR011095<br />InterPro:IPR011127<br />SP_KW:KW-0573<br />HAMAP:MF_00047
SP_KW:KW-0067
|
|
P
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 164: Line 259:
cell wall
cell wall
|
|
PMID:9220001
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011127
|
|
IDA: Inferred from Direct Assay
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_00047
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|


|
GO:0005737
|
cytoplasm
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005905
|
|
C
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  
complete  
Line 183: Line 335:
cytoplasm
cytoplasm
|
|
GO_REF:0000002<br />GO_REF:0000004
GO_REF:0000023
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR005905<br />SP_KW:KW-0963
SP_SL:SL-0086
|
|
C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 200: Line 352:
GO:0007047
GO:0007047
|
|
cell wall organization
cellular cell wall organization
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 210: Line 362:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 221: Line 373:
regulation of cell shape
regulation of cell shape
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 229: Line 381:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 240: Line 392:
D-alanine-D-alanine ligase activity
D-alanine-D-alanine ligase activity
|
|
PMID:8756703
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_00047
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
IMP: Inferred from Mutant Phenotype
complete
|-
|
|


|
GO:0008716
|
D-alanine-D-alanine ligase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000291
|
|
F
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|


|
GO:0008716
|
D-alanine-D-alanine ligase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005905
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 255: Line 445:


|
|
GO:0000166
GO:0008716
|
D-alanine-D-alanine ligase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011095
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008716
|
|
nucleotide binding
D-alanine-D-alanine ligase activity
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0547
InterPro:IPR011127
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 274: Line 483:


|
|
GO:0000287
GO:0008716
|
|
magnesium ion binding
D-alanine-D-alanine ligase activity
|
|
GO_REF:0000004
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0460
EC:6.3.2.4
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009252
|
peptidoglycan biosynthetic process
|
GOA:hamap<br />GO_REF:0000020
|
IEA: Inferred from Electronic Annotation
|
HAMAP:MF_00047
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009252
|
peptidoglycan biosynthetic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000291
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009252
|
peptidoglycan biosynthetic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005905
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009252
|
peptidoglycan biosynthetic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011095
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009252
|
peptidoglycan biosynthetic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011127
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009252
|
peptidoglycan biosynthetic process
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0573
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 297: Line 620:
manganese ion binding
manganese ion binding
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 305: Line 628:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 316: Line 639:
metal ion binding
metal ion binding
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 324: Line 647:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0000910
GO:0008716
|
|
cytokinesis
D-alanine-D-alanine ligase activity
|
|
PMID:1554356
|
|
IDA: Inferred from Direct Assay
|
|
 
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Table 1, Fig. 3
|
|
required fields missing 
complete
|-  
|-  
|
|
Line 362: Line 685:
F
F
|
|
 
Tables II and III
|
|
complete  
complete  


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|<div class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19669.R46aa1b41b7235&page=19669&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</div> || || || || || || || ||
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<!--box uid=421aa90e079fa326b6494f812ad13e79.19669.R46aa1b41b7235-->
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*  
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****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   id="C46aa1b4fd68aa"  class=" tableEdit Product_interactions_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46aa1b4fd68aa"  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 411: Line 734:
*  
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****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="F46aa1b50dd8cb"  class=" tableEdit Product_localization_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46aa1b50dd8cb"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-  
|-  
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****************************************************************************************** -->{{Product_physical_properties_help}}
{| id="S46aa1b524dfd4"  class=" tableEdit Product_phys_prop_table"   
{|   id="S46aa1b524dfd4"  class=" tableEdit Product_phys_prop_table"   
 
|-
!align=left {{table heading style}} |Name
||


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{|   id="S46aa1b52a663a"  class=" tableEdit Product_motif_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46aa1b52a663a"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
Line 505: Line 832:
|
|
   
   
|-
|
Domain
|
3..54
|
[http://pfam.janelia.org/family/PF01820 PF01820  D-ala D-ala ligase N-terminus]
|
|
PMID:19920124
|-
|
Domain
|
43..86
|
[http://pfam.janelia.org/family/PF01820 PF01820  D-ala D-ala ligase N-terminus]
|
|
PMID:19920124
|-
|
Domain
|
103..303
|
[http://pfam.janelia.org/family/PF07478 PF07478  D-ala D-ala ligase C-terminus]
|
|
PMID:19920124


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{|   id="E46aa1b52ef35b"  class=" tableEdit Product_structure_table"   


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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/P07862 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=P07862 PSI-PRED (P07862)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P07862 Genomes TO Protein (P07862)] (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)


|- class="tableEdit_footer"  
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****************************************************************************************** -->{{Product_resources_help}}
{|   id="J46aa1b54ab249"  class=" tableEdit Product_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46aa1b54ab249"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
Line 607: Line 965:
*  
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****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="B46aa1b54f41b4"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46aa1b54f41b4"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=DALADALALIGB-MONOMER EcoCyc:DALADALALIGB-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16128085 GI:16128085]
|
|
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_414634.1 GeneID:946324]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000326
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P07862 UniProtKB/Swiss-Prot:P07862]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG10214
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG10214
|
''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:P07862|UniProt:P07862]]
[http://www.ncbi.nlm.nih.gov/gene?term=946324 GeneID:946324]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.sanger.ac.uk/family?acc=PF01820 PFAM:PF01820]
RegulonDB:ECK120000208
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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]])
[[EchoBASE]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414634 RefSeq:NP_414634]
EchoBASE:EB0210
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0009252_!_peptidoglycan biosynthetic process]][[Category:GO:0000910_!_cytokinesis]][[Category:Complex:D-alanine-D-alanine ligase B]][[Category:Location:cytoplasm]][[Category:Products with structures in PDB]]

Latest revision as of 23:32, 18 May 2019

{{#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

DdlB

Synonyms

D-alanine:D-alanine ligase[1], B0092[2][1], Ddl[2][1], DdlB[2][1] , ddl, ECK0093, JW0090, b0092

Product description

ddlB[2][3];

Component of D-alanine-D-alanine ligase B[2][3]

D-alanine:D-alanine ligase B, ADP-forming[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:0008716

D-alanine-D-alanine ligase activity

PMID:8756703[5]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1993184[6]

IDA: Inferred from Direct Assay

F

Tables II and III

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013816

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013817

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016185

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005618

cell wall

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

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:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000291

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011095

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.3.2.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000291

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011095

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

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

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1554356[7]

IDA: Inferred from Direct Assay

F

Table 1, Fig. 3

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1993184[6]

IDA: Inferred from Direct Assay

F

Tables II and III

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

Subunits of D-alanine-D-alanine ligase B

could be indirect


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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

cytoplasm

From EcoCyc[3]


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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 

MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI
ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA
EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE
KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL
VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR
ILELAD
Length

306

Mol. Wt

32.84 kDa

pI

4.6 (calculated)

Extinction coefficient

37,930 - 38,180 (calc based on 7 Y, 5 W, and 2 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:P07862

Domain

3..54

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124[8]

Domain

43..86

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124[8]

Domain

103..303

PF07478 D-ala D-ala ligase C-terminus

PMID:19920124[8]

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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=ddlB 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:16128085

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000326

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P07862

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10214

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10214

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000208

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0210

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 2.3 2.4 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 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. ↑ Park, IS et al. (1996) Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B. Biochemistry 35 10464-71 PubMed
  6. ↑ 6.0 6.1 Zawadzke, LE et al. (1991) Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes. Biochemistry 30 1673-82 PubMed
  7. ↑ al-Bar, OA et al. (1992) D-alanine: D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme. Biochem. J. 282 ( Pt 3) 747-52 PubMed
  8. ↑ 8.0 8.1 8.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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