scpB:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
methylmalonyl-CoA decarboxylase, biotin-independent<ref name='LIB:Riley_2006'/>, B2919<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgfG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''methylmalonyl-CoA decarboxylase, biotin-independent<ref name='LIB:Riley_2006'/>, B2919<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgfG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2915, JW2886, mmcD, ygfG, b2919''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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Component of [[:Category:Complex:methylmalonyl-CoA decarboxylase|methylmalonyl-CoA decarboxylase]]<ref name='LIB:EcoCyc11.1'/>
Component of [[:Category:Complex:methylmalonyl-CoA decarboxylase|methylmalonyl-CoA decarboxylase]]<ref name='LIB:EcoCyc11.1'/>


Methylmalonyl-CoA decarboxylase<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=4.1.1.41 4.1.1.41]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.41 4.1.1.41]<ref name='LIB:Riley_2006'/>


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|- {{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
|-  
|-  
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|


|
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GO:0016829
GO:0005737
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|
lyase activity
cytoplasm
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GO_REF:0000004
 
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|
IEA: Inferred from Electronic Annotation
 
|
|
SP_KW:KW-0456
 
|
|
F
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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|
complete
Missing: evidence, reference
|-  
|-  
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|
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GO:0008152
GO:0004492
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metabolic process
methylmalonyl-CoA decarboxylase activity
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GO_REF:0000002
GOA:spec<br />GO_REF:0000003
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR001753
EC:4.1.1.41
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P
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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GO:0004492
GO:0008152
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methylmalonyl-CoA decarboxylase activity
metabolic process
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GO_REF:0000003
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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EC:4.1.1.41
InterPro:IPR001753
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F
P
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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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GO:0003824
GO:0008152
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catalytic activity
metabolic process
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GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR001753
InterPro:IPR018376
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F
P
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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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GO:0005737
GO:0004492
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cytoplasm
methylmalonyl-CoA decarboxylase activity
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PMID:10769117
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IDA: Inferred from Direct Assay
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|
 
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C
F
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Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
 
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required fields missing 
complete


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
||


|-
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ITAQRALAVG ILNHVVEVEE LEDFTLQMAH HISEKAPLAI AVIKEELRVL GEAHTMNSDE
ITAQRALAVG ILNHVVEVEE LEDFTLQMAH HISEKAPLAI AVIKEELRVL GEAHTMNSDE
FERIQGMRRA VYDSEDYQEG MNAFLEKRKP NFVGH</pre>  
FERIQGMRRA VYDSEDYQEG MNAFLEKRKP NFVGH</pre>  
|-
!align=left {{table heading style}} |Length
||
275
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
29.17 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
30.83 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.6 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
15930 - 16055 (calc based on 7 Y, 1 W, and 1 C residues)  
15,930 - 16,055 (calc based on 7 Y, 1 W, and 1 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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<!--
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|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
15..183
|
[http://pfam.janelia.org/family/PF00378 PF00378  Enoyl-CoA hydratase/isomerase family]
|
 
|
PMID:19920124


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


<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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|-
|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>scpB
<beststructure>
562</beststructure>
gene=scpB
 
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=scpB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P52045 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=scpB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P52045 PSI-PRED (P52045)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P52045 Genomes TO Protein (P52045)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/90111512 GI:90111512]
|
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_417394.4 GeneID:947408]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0009581
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7516-MONOMER EcoCyc:G7516-MONOMER]
[http://www.uniprot.org/uniprot/P52045 UniProtKB/Swiss-Prot:P52045]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoCyc]]
|
|
[[uniprot:P52045|UniProt:P52045]]
EcoCyc:G7516
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00378 PFAM:PF00378]
EcoGene:EG12972
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417394 RefSeq:NP_417394]
[http://www.ncbi.nlm.nih.gov/gene?term=947408 GeneID:947408]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P52045 ModBase:P52045]
RegulonDB:ECK120004078
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EF8 PDB:1EF8]
EchoBASE:EB2799
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
===Categories===
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[[Category:GO:0005737_!_cytoplasm]][[Category:Complex:methylmalonyl-CoA decarboxylase]][[Category:Products with structures in PDB]]
[[Category:Proteins]]

Latest revision as of 20:57, 17 February 2015

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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

YgfG

Synonyms

methylmalonyl-CoA decarboxylase, biotin-independent[1], B2919[2][1], YgfG[2][1] , ECK2915, JW2886, mmcD, ygfG, b2919

Product description

YgfG[2]; ScpB[3];

Component of methylmalonyl-CoA decarboxylase[3]

Methylmalonyl-CoA decarboxylase[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0004492

methylmalonyl-CoA decarboxylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.41

F

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001753

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018376

P

Seeded from EcoCyc (v14.0)

complete

GO:0004492

methylmalonyl-CoA decarboxylase activity

PMID:10769117[5]

IDA: Inferred from Direct Assay

F

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 methylmalonyl-CoA decarboxylase

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
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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 

MNLSRRNILI KGIFMSYQYV NVVTINKVAV IEFNYGRKLN ALSKVFIDDL MQALSDLNRP
EIRCIILRAP SGSKVFSAGH DIHELPSGGR DPLSYDDPLR QITRMIQKFP KPIISMVEGS
VWGGAFEMIM SSDLIIAAST STFSMTPVNL GVPYNLVGIH NLTRDAGFHI VKELIFTASP
ITAQRALAVG ILNHVVEVEE LEDFTLQMAH HISEKAPLAI AVIKEELRVL GEAHTMNSDE
FERIQGMRRA VYDSEDYQEG MNAFLEKRKP NFVGH
Length

275

Mol. Wt

30.83 kDa

pI

6.6 (calculated)

Extinction coefficient

15,930 - 16,055 (calc based on 7 Y, 1 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 Notes References

Domain

15..183

PF00378 Enoyl-CoA hydratase/isomerase family

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=scpB 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:90111512

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947408

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009581

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52045

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7516

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12972

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004078

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2799

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. ↑ 3.0 3.1 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. ↑ Haller, T et al. (2000) Discovering new enzymes and metabolic pathways: conversion of succinate to propionate by Escherichia coli. Biochemistry 39 4622-9 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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