sucA:Gene Product(s): Difference between revisions

Standard name	SucA
Synonyms	2-oxoglutarate decarboxylase, thiamin-requiring^[1] , ECK0714, JW0715, lys, b0726
Product description	2-oxoglutarate dehydrogenase, E1 component; yields succinyl-CoA and CO(2)^[2]
EC number (for enzymes)	1.2.4.2^[1]
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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:0006099	tricarboxylic acid cycle				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0004591	oxoglutarate dehydrogenase (succinyl-transferring) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011603	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004591	oxoglutarate dehydrogenase (succinyl-transferring) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.2.4.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726^[3]	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006096	glycolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011603	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006096	glycolysis	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0324	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001017	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016624	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001017	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030976	thiamin pyrophosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011603	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	hflK		PMID:15690043^[4]	Experiment(s):EBI-880717
Protein	lipA		PMID:15690043^[4]	Experiment(s):EBI-880717
Protein	lpdA		PMID:15690043^[4]	Experiment(s):EBI-880717, EBI-886788
Protein	sucB		PMID:15690043^[4]	Experiment(s):EBI-880717, EBI-880739, EBI-886788
Protein	groL		PMID:16606699^[5]	Experiment(s):EBI-1137802
Protein	dnaE		PMID:16606699^[5]	Experiment(s):EBI-1137802
Protein	oxc		PMID:16606699^[5]	Experiment(s):EBI-1137802
Protein	rplC		PMID:15690043^[4]	Experiment(s):EBI-886788
Protein	lipA		PMID:19402753^[6]	MALDI(Z-score):25.667279
Protein	sucB		PMID:19402753^[6]	LCMS(ID Probability):99.6 MALDI(Z-score):33.552055
Small Molecule	TTTPP	selectively inhibits pyruvate or 2-oxoglutarate dehydrogenase (El).
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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	MRITIILVAP ARAENIGAAA RAMKTMGFSD LRIVDSQAHL EPATRWVAHG SGDIIDNIKV FPTLAESLHD VDFTVATTAR SRAKYHYYAT PVELVPLLEE KSSWMSHAAL VFGREDSGLT NEELALADVL TGVPMVADYP SLNLGQAVMV YCYQLATLIQ QPAKSDATAD QHQLQALRER AMTLLTTLAV ADDIKLVDWL QQRLGLLEQR DTAMLHRLLH DIEKNITK
Length	228
Mol. Wt	25.259 kDa
pI	5.9 (calculated)
Extinction coefficient	25,440 - 25,565 (calc based on 6 Y, 3 W, and 1 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	References
Domain	589..785	PF02779 Transketolase, pyrimidine binding domain	PMID:19920124^[7]
Domain	207..516	PF00676 Dehydrogenase E1 component	PMID:19920124^[7]
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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=sucA taxon=562,83333 </beststructure>

Models

View models at:

PSI-PRED (P0AFG3)
Genomes TO Protein (P0AFG3) (GTOP)

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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:16128701	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945303	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002478	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFG3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10979	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10979	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945303	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000968	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0972	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.0 ^1.1 ^1.2 ^1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^5.0 ^5.1 ^5.2 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^6.0 ^6.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ ^7.0 ^7.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
--oxoglutarate decarboxylase, thiamin-requiring<ref name='LIB:Riley_2006'/>
+''2-oxoglutarate decarboxylase, thiamin-requiring<ref name='LIB:Riley_2006'/> , ECK0714, JW0715, lys, b0726''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 75: / Line 75: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{| {{Prettytable}}  id="Q46aa3fb870112"  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="Q46aa3fb870112"  class=" tableEdit GO_table_product dataTable"
 |- {{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 96: / Line 96: @@
 Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
 |
-Missing: evidence
+Missing: evidence, reference
 |-
 |
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 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="R46aa3fbbdfa3d"  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="R46aa3fbbdfa3d"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 411: / Line 411: @@
 |
 Experiment(s):EBI-886788<br />
+|-
+|
+Protein
+|
+lipA
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):25.667279
+|-
+|
+Protein
+|
+sucB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):33.552055
 |-
 |
@@ Line 440: / Line 462: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="R46a7d169ba147"  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="R46a7d169ba147"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
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 ****************************************************************************************** -->{{Product_physical_properties_help}}
 {|   id="N46aa3fbda1572"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
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 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="C46aa3fbe08532"  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="C46aa3fbe08532"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
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 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AFG3 PSI-PRED (P0AFG3)]
-* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AFG3 Genomes TO Protein (P0AFG3)] (GTOP)
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
-* [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="F46aa3fbea00f6"  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="F46aa3fbea00f6"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 633: / Line 656: @@
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 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="N46a7d16be0e7d"  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="N46a7d16be0e7d"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
+|-
+|
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/16128701 GI:16128701]
+|
+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_415254.1 GeneID:945303]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0002478
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P0AFG3 UniProtKB/Swiss-Prot:P0AFG3]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:EG10979
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG10979
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/gene?term=945303 GeneID:945303]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[RegulonDB]]
+|
+RegulonDB:ECK120000968
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EchoBASE]]
+|
+EchoBASE:EB0972
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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-{|   id="Y46a7d16c264db"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a7d16c264db"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments

sucA:Gene Product(s): Difference between revisions

Latest revision as of 20:29, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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sucA:Gene Product(s): Difference between revisions

Latest revision as of 20:29, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

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