rhmA:Gene Product(s): Difference between revisions

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{{Tab|Quickview|yfaU}}{{Tab|Gene|yfaU}}{{Tab On|Gene Product(s)|yfaU}}{{Tab|Expression|yfaU}}{{Tab|Evolution|yfaU}}{{Tab|On One Page|yfaU}}{{TabsBottom}}
{{Tab|Quickview|rhmA}}{{Tab|Gene|rhmA}}{{Tab On|Gene Product(s)|rhmA}}{{Tab|Expression|rhmA}}{{Tab|Evolution|rhmA}}{{Tab|On One Page|rhmA}}{{TabsBottom}}
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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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|-
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!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
YfaU product
RhmA
|-
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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predicted 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase product<ref name='LIB:Riley_2006'/>, B2245 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfaU product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase<ref name='LIB:Riley_2006'/>, B2245<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RhmA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2238, JW2239, yfaU, b2245''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
||
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predicted aldolase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
predicted aldolase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>.  Crystal structure shows that RhmA is a
metal-dependent class II aldolase belonging
metal-dependent class II aldolase belonging
to the pyruvate/enolpyruvate binding (�/R)8 barrel superfamily.<ref name='PMID:18754683 '/>, Genomic context suggested a 2-dehydro-3-deoxy
to the pyruvate/enolpyruvate binding (�/R)8 barrel superfamily.<ref name='PMID:18754683 '/>, Genomic context suggested a 2-dehydro-3-deoxy
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Functional assignment of YfaW as a L-rhamnonate dehydratase
Functional assignment of YfaW as a L-rhamnonate dehydratase
suggested 2-dehydro-3-deoxy-L-rhamnonate is the
suggested 2-dehydro-3-deoxy-L-rhamnonate is the
physiological substrate of YfaU, and enzyme kinetic measurements
physiological substrate of RhmA, and enzyme kinetic measurements
support this assignment.
support this assignment.


Putative HHED aldolase, function unknown<ref name='LIB:EcoGene'/>
|-
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!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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*


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===Notes===
===Notes===
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<protect>
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.24677.A46aa9b9562e26-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.24677.A46aa9b9562e26-->
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{|   id="A46aa9b9562e26" class=" tableEdit GO_table_product dataTable"   
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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:0003824_!_catalytic_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003824_!_catalytic_activity GO:0003824]
GO:0000287
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|
catalytic_activity
magnesium ion binding
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|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000002 GO_REF:0000002]<br />
GOA:spkw<br />SP_KW:GO_REF:0000004
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR015813
SP_KW:KW-0460
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F
|
Seeded from [[EcoCyc]] (v14.0)
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complete
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|
 
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GO:0005515
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protein binding
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PMID:18754683
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IPI: Inferred from Physical Interaction
|
 
|
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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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Missing: with/from
|-  
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[[Category:GO:0006725_!_cellular_aromatic_compound_metabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006725_!_cellular_aromatic_compound_metabolic_process GO:0006725]
GO:0006725
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|
aromatic_compound_metabolism
cellular aromatic compound metabolic process
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[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000002 GO_REF:0000002]<br />
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
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|
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[[Category:GO:0016829_!_lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016829_!_lyase_activity GO:0016829]
GO:0016151
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|
lyase_activity
nickel ion binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000004 GO_REF:0000004]<br />
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-0533
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
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|
|
 
|
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[[Category:GO:0008152_!_metabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008152_!_metabolic_process GO:0008152]
GO:0016832
|
|
metabolic process
aldehyde-lyase activity
|
|
GOA:hamap<br />GO_REF:0000020
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|
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01290
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
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|
|


|
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[[Category:GO:0016830_!_carbon-carbon_lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016830_!_carbon-carbon_lyase_activity GO:0016830]
GO:0016832
|
|
carbon-carbon_lyase_activity
aldehyde-lyase activity
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|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000002 GO_REF:0000002]<br />
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR005000
EC:4.1.2
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0000287
|
magnesium ion binding
|
PMID:18754683
|
IPI: Inferred from Physical Interaction
|
 
|
F
|
 
|
Missing: with/from
|-
|
 
|
GO:0006725
|
cellular aromatic compound metabolic process
|
PMID:18754683
|
ISS: Inferred from Sequence or Structural Similarity
|
UniProtKB:Q47098
|
P
|
 
|
complete
|-
|
 
|
GO:0016151
|
nickel ion binding
|
PMID:18754683
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0016832
|
aldehyde-lyase activity
|
PMID:18754683
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
 
|
GO:0005737
|
cytoplasm
|
PMID:18754683
|
IDA: Inferred from Direct Assay
|
 
|
C
|
 
|
complete
|-
|
 
|
GO:0005515
|
protein binding
|
PMID:18754683
|
IPI: Inferred from Physical Interaction
|
EcoliWiki:yfaU
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
 
|
|
complete


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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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{|{{Prettytable}}
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!align=left {{table heading style}} |Name
||
 
|-
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
|
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[http://biocyc.org/ECOLI/sequence-aa?object=G7158-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G7158-MONOMER at EcoCyc]  
<pre>MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA PNTIQDLYHQ
<pre>MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA PNTIQDLYHQ
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MLYSDALDQR LAMFKSGKNG PRIKGSY</pre>  
MLYSDALDQR LAMFKSGKNG PRIKGSY</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
||
28.92 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
267
|-
|-
!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
28.916 kDa
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
36900 - 37150 (calc based on 10 Y, 4 W, and 2 C residues)  
5.2 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
36,900 - 37,150 (calc based on 10 Y, 4 W, and 2 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
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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=421aa90e079fa326b6494f812ad13e79.24677.C46aa9b9ac3935-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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Domain
|
19..246
|
[http://pfam.janelia.org/family/PF03328 PF03328  HpcH/HpaI aldolase/citrate lyase 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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!|Structures!!Models
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!align=left {{table heading style}} |Structures
|
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1.39 A structure of apo-YfaU and the Mg2+-pyruvate product complex
<beststructure>
<ref name='PMID:18754683'/>
gene=yfaU
|
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P76469 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76469 PSI-PRED (P76469)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76469 Genomes TO Protein (P76469)] (GTOP)


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


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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16130180 GI:16130180]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_416748.1 GeneID:948054]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[ASAP]]
|
ASAP:ABE-0007431
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7158-MONOMER EcoCyc:G7158-MONOMER]
[http://www.uniprot.org/uniprot/P76469 UniProtKB/Swiss-Prot:P76469]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P76469 SwissModel:P76469] 
EcoCyc:G7158
|
|
''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:P76469|UniProt:P76469]] 
EcoGene:EG14083
|
|
''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=PF03328 PFAM:PF03328]
[http://www.ncbi.nlm.nih.gov/gene?term=948054 GeneID:948054]
|
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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_416748 RefSeq:NP_416748] 
RegulonDB:ECK120003734
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P76469 ModBase:P76469] 
EchoBASE:EB3836
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0008152_!_metabolic process]]

Latest revision as of 16:36, 5 October 2013

{{#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

RhmA

Synonyms

predicted 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase[1], B2245[2][1], RhmA[2][1] , ECK2238, JW2239, yfaU, b2245

Product description

predicted aldolase[2][3]. Crystal structure shows that RhmA is a metal-dependent class II aldolase belonging to the pyruvate/enolpyruvate binding (�/R)8 barrel superfamily.[4], Genomic context suggested a 2-dehydro-3-deoxy sugar aldolase function rather than the 4-hydroxy-2-ketoheptane- 1,7-dioate aldolase function as annotated in the databases based on homology with the related HpcH. Functional assignment of YfaW as a L-rhamnonate dehydratase suggested 2-dehydro-3-deoxy-L-rhamnonate is the physiological substrate of RhmA, and enzyme kinetic measurements support this assignment.

Putative HHED aldolase, function unknown[5]

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: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:0005515

protein binding

PMID:18754683[4]

IPI: Inferred from Physical Interaction

F

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0006725

cellular aromatic compound metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005000

P

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0533

F

Seeded from EcoCyc (v14.0)

complete

GO:0016832

aldehyde-lyase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01290

F

Seeded from EcoCyc (v14.0)

complete

GO:0016832

aldehyde-lyase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

PMID:18754683[4]

IPI: Inferred from Physical Interaction

F

Missing: with/from

GO:0006725

cellular aromatic compound metabolic process

PMID:18754683[4]

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:Q47098

P

complete

GO:0016151

nickel ion binding

PMID:18754683[4]

IDA: Inferred from Direct Assay

F

complete

GO:0016832

aldehyde-lyase activity

PMID:18754683[4]

IDA: Inferred from Direct Assay

F

complete

GO:0005737

cytoplasm

PMID:18754683[4]

IDA: Inferred from Direct Assay

C

complete

GO:0005515

protein binding

PMID:18754683[4]

IPI: Inferred from Physical Interaction

EcoliWiki:yfaU

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
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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 

MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA PNTIQDLYHQ
LQAVAPYASQ PVIRPVEGSK PLIKQVLDIG AQTLLIPMVD TAEQARQVVS ATRYPPYGER
GVGASVARAA RWGRIENYMA QVNDSLCLLV QVESKTALDN LDEILDVEGI DGVFIGPADL
SASLGYPDNA GHPEVQRIIE TSIRRIRAAG KAAGFLAVAP DMAQQCLAWG ANFVAVGVDT
MLYSDALDQR LAMFKSGKNG PRIKGSY
Length

267

Mol. Wt

28.916 kDa

pI

5.2 (calculated)

Extinction coefficient

36,900 - 37,150 (calc based on 10 Y, 4 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

Domain

19..246

PF03328 HpcH/HpaI aldolase/citrate lyase 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=yfaU 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:16130180

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948054

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007431

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76469

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7158

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14083

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948054

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003734

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3836

Escherichia coli str. K-12 substr. MG1655

edit table


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 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. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 Rea, D et al. (2008) Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochemistry 47 9955-65 PubMed
  5. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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